Assay Cartridges and Methods of Using the Same

ABSTRACT

Assay cartridges are described that have purification, reaction, and detection zones and other fluidic components which can include sample chambers, waste chambers, conduits, vents, reagent chambers, reconstitution chambers and the like. The assay cartridges are used to conduct multiplexed nucleic acid measurements. Also described are kits including such cartridges, methods of using the same, and a reader configured to analyze an assay conducted using an assay cartridge.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.61/460,708 filed on Jan. 6, 2011, the entire contents of which areincorporated herein by reference.

STATEMENT REGARDING FEDERALLY-SPONSORED RESEARCH

This invention was made with federal support under W911NF-06-C-0120 fromthe Defense Threat Reduction Agency and W81XWH-10-2-0155 from theCongressionally Directed Medical Research Program. The U.S. governmenthas certain rights in the invention.

FIELD OF THE INVENTION

This application relates to apparatuses, systems, kits and methods forconducting multiplexed nucleic acid measurements on a sample. Theseapparatuses include assay cartridges and readers for conducting theseassays.

BACKGROUND OF THE INVENTION

Amplified nucleic acid assays for pathogens can achieve sensitivitiesapproaching single organism detection. Practical considerations, inparticular the need for time consuming, labor intensive, and complexsample preparation, have prevented wide spread application of amplifiednucleic acid assays in field or point-of-care settings. In addition,there is a need for amplified nucleic acid assays with high levels ofmultiplexing that can detect multiple different organisms in a sample.

SUMMARY OF THE INVENTION

The invention provides an assay cartridge comprising a chamber and afluidic network including: (a) a primary flow path comprising, from aproximate to a distal end, an inlet, a purification zone, a reactionzone, and a detection zone, wherein the primary flow path furthercomprises one or more air vent ports, and (b) one or more fluidicconduits each intersecting the primary flow path and fluidicallyconnected to the chamber, wherein the chamber is connected to anadditional air vent port, wherein the fluidic network is configured tometer a volume of fluid in the primary flow path. Preferably, a fluidicconduit of the one or more fluidic conduits comprises a multi-conduitfluidic junction including (i) a first conduit connecting the primaryflow path and the chamber, and (ii) a second conduit connecting thechamber to the additional air vent port, wherein the fluidic conduit isin communication with an optical fluid sensor at a position distal fromthe fluidic junction and the metered volume of fluid is defined by thedistance between the fluidic junction and the distal position.

Also provided is an assay system comprising an assay cartridge and areader configured to use the assay cartridge, wherein the assaycartridge comprises a chamber and a fluidic network including (a) aprimary flow path comprising, from a proximate to a distal end, aninlet, a purification zone, a reaction zone, and a detection zone,wherein the primary flow path further comprises one or more air ventports, and (b) one or more fluidic conduits each intersecting theprimary flow path and fluidically connected to the chamber, wherein thechamber is connected to an additional air vent port; wherein the fluidicnetwork is configured to meter a volume of fluid in the primary flowpath; and the reader comprises (x) an enclosure; (y) a cartridge trayfor holding the cartridge during analysis in the reader; and (z) amounting frame in the enclosure, the mounting frame is configured toalign the cartridge with one or more reader components comprise (i) anoptical detection assembly comprising at least one CCD detector; (ii) anampoule breaking mechanism; (iii) an electrode contact pin assembly;(iv) a fluidic control manifold configured to drive fluid motion withinthe fluidic network; (v) one or more heater assemblies; and/or (vi) oneor more optical fluid sensors.

In a preferred embodiment, the invention provides an assay cartridge forconducting a PCR analysis of a sample, the cartridge comprising achamber and a fluidic network including (a) a primary flow pathcomprising, from a proximate to a distal end, an inlet, a purificationzone, a PCR reaction zone, and a detection zone, wherein the primaryflow path further comprises one or more air vent ports, and (b) one ormore fluidic conduits each intersecting the primary flow path andfluidically connected to the chamber, wherein the chamber is connectedto an additional air vent port, and the PCR reaction zone comprises afirst reaction temperature controlled zone and a second reactiontemperature controlled zone and the fluidic network is configured toshuttle a metered volume of fluid between the first and second reactiontemperature controlled zones during a PCR reaction conducted in the PCRreaction zone. Preferably, a fluidic conduit of the one or more fluidicconduits comprises a multi-conduit fluidic junction including (i) afirst conduit connecting the primary flow path and the chamber, and (ii)a second conduit connecting the chamber to the additional air vent port,wherein the fluidic conduit is in communication with an optical fluidsensor at a position distal from the fluidic junction and the meteredvolume of fluid is defined by the distance between the fluidic junctionand the distal position.

The invention also provides an assay cartridge for conducting a PCRanalysis of a sample, the cartridge comprising a fluidic network and aplurality of chambers, wherein the fluidic network comprises (a) aprimary flow path comprising, from a proximate to a distal end, aninlet, a purification zone, a PCR reaction zone, and a detection zone,wherein the primary flow path further comprises one or more air ventports, and (b) one or more fluidic conduits each intersecting theprimary flow path and fluidically connected to one or more of thechambers, wherein each of the chambers are connected to an additionalair vent port, wherein the plurality of chambers include: a samplechamber, a lysis reagent chamber, a lysis chamber, a purificationreagent chamber, a plurality of PCR reagent chambers, a plurality ofreconstitution chambers, and one or more waste chambers; and the PCRreaction zone comprises a first reaction temperature controlled zone anda second reaction temperature controlled zone and the fluidic network isconfigured to shuttle a metered volume of fluid between the first andsecond reaction temperature controlled zones during a PCR reactionconducted in the PCR reaction zone. Preferably, a fluidic conduit of theone or more fluidic conduits comprises a multi-conduit fluidic junctionincluding (i) a first conduit connecting the primary flow path and thechamber, and (ii) a second conduit connecting the chamber to theadditional air vent port, wherein the fluidic conduit is incommunication with an optical fluid sensor at a position distal from thefluidic junction and the metered volume of fluid is defined by thedistance between the fluidic junction and the distal position.

A further embodiment of the invention is a method of conducting a PCRanalysis of a sample in an assay cartridge, the cartridge comprising afluidic network and a plurality of chambers, wherein the fluidic networkcomprises (a) a primary flow path comprising, from a proximate to adistal end, (i) an inlet, (ii) a purification zone, (iii) a PCR reactionzone including a first reaction temperature controlled zone and a secondreaction temperature controlled zone, and (iv) a detection zone, whereinthe primary flow path further comprises (vi) one or more air vent ports,and (b) one or more fluidic conduits each intersecting the primary flowpath and fluidically connected to one or more of the chambers, whereineach of the chambers are connected to an additional air vent port,wherein the plurality of chambers include: a sample chamber, a lysisreagent chamber, a lysis chamber, a purification reagent chamber, aplurality of PCR reagent chambers, and one or more waste chambers; themethod comprising the steps of:

(i) metering a volume of sample from the sample chamber to the lysischamber;

(ii) metering a volume of lysis buffer from the lysis reagent chamber tothe lysis chamber;

(iii) lysing the volume of sample;

(iv) moving the lysate from the lysis chamber to the purification zone;

(v) extracting nucleic acid from the lysate;

(vi) purifying the nucleic acid;

(vii) moving the a purified nucleic acid mixture to the PCR reactionzone;

(viii) contacting the purified nucleic acid mixture with one or more PCRreagents;

(ix) shuttling the mixture formed in step (viii) between the first andsecond reaction temperature controlled zones;

(ix) repeating steps (viii) and (ix) to form an amplified productmixture;

(x) contacting the amplified product mixture with a detection reagent;

(xi) moving the mixture formed in step (x) to the detection zone; and

(xii) measuring a signal from the detection zone.

Another embodiment of the invention is an assay cartridge configured topurify components of a sample, the assay cartridge comprising a primaryfluid path including a purification zone, a purification reagentchamber, and a waste chamber, wherein the purification zone comprises,from a proximal to a distal end, (i) a purification multi-conduitfluidic junction including (a) a first purification reagent chamberconduit connecting the primary flow path and the purification reagentchamber; and (b) a second purification reagent chamber conduitconnecting the purification reagent chamber and a purification reagentchamber air vent port; (ii) an integrated purification membranepositioned in the purification zone; and (iii) a waste multi-conduitfluidic junction including (a) a first waste chamber conduit connectingthe primary flow path and the waste chamber; and (b) a second wastechamber conduit connecting the waste chamber and a waste chamber airvent port.

Moreover, the invention contemplates a method of purifying a fluid in anassay cartridge comprising a primary fluid path including a purificationzone, a purification reagent chamber, and a waste chamber, wherein thepurification zone comprises, from a proximal to a distal end, (i) apurification multi-conduit fluidic junction including (a) a firstpurification reagent chamber conduit connecting the primary flow pathand the purification reagent chamber; and (b) a second purificationreagent chamber conduit connecting the purification reagent chamber anda purification reagent chamber air vent port; (ii) an integratedpurification membrane positioned in the purification zone; and (iii) awaste multi-conduit fluidic junction including (a) a first waste chamberconduit connecting the primary flow path and the waste chamber; and (b)a second waste chamber conduit connecting the waste chamber and a wastechamber air vent port; the method comprising the steps of:

(x) moving a volume of fluid through the membrane;

(y) removing a volume of fluid eluted in step (x) to the waste chamber;

(z) moving one or more volumes of purification reagent from thepurification reagent chamber through the membrane;

(xx) removing one or more volumes of fluid eluted in step (z) to thewaste chamber; and

(yy) eluting a purified volume of fluid from the membrane.

The invention further provides an assay cartridge configured to conducta reaction using a sample processed in the cartridge, the assaycartridge comprising a primary flow path including a reaction zone,wherein the reaction zone comprises a first reaction temperaturecontrolled zone and a second reaction temperature controlled zone andthe primary flow path is configured to shuttle a volume of fluid betweenthe first and second reaction temperature controlled zones during areaction conducted in the reaction zone, wherein the primary flow pathis intersected at the reaction zone by one or more reagent multi-conduitjunctions connecting (i) the primary flow path and one or more reactionreagent chambers; and (ii) the one or more reagent chambers and one ormore reagent chamber air vent ports.

In addition, the invention provides an assay cartridge configured todetect a component of a metered volume of fluid in the cartridge, thecartridge comprising a one or more detection reagent chambers and aprimary flow path including a detection zone, wherein the detection zoneis intersected by a detection reagent multi-conduit junction connecting(i) the primary flow path and the one or more detection reagentchambers; and (ii) the one or more detection reagent chambers and one ormore detection reagent air vent ports.

Moreover, the invention includes a fluidic network comprising a chamberconnected to an air vent port, the fluidic network comprising a primaryflow path and one or more fluidic conduits each intersecting the primaryflow path and fluidically connecting the primary flow path to thechamber, wherein the fluidic network is configured to meter a volume offluid in the network. Also provided is a system configured to interfacewith a fluidic network as described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1( a) is a schematic representation of the fluidic network andreagent storage and processing zones within the cartridge.

FIG. 1( b) is a schematic representation of a multi-conduit fluidicjunction.

FIG. 2( a) is one embodiment of a cartridge of the invention configuredto conduct multiplexed nucleic acid measurements and sample processing,including nucleic acid extraction, purification, amplification, anddetection of PCR amplicons.

FIGS. 2( b-c) show the position of vent ports in one embodiment of acartridge of the invention. FIG. 2( c) is a cross-sectional view of themanifold interface port shown in FIG. 2( b), which depicts an aerosolbarrier incorporated into the cartridge at the point where the manifoldmates with the cartridge.

FIG. 3( a) is a detailed flow diagram of the operation of the cartridgedepicted in FIG. 2( a).

FIG. 3( b) shows one embodiment of a lysis chamber, including an inletport and a series of “Z transitions” at the exit of the lysis chamberfor mixing the sample and lysis buffer.

FIGS. 3( c-d) depict cross-sectional views of an embodiment of thedesign for an extraction filter used in the purification zone. Panel (c)shows that the design is composed of three components, i.e., a top, GFDfilter, and base. The top carrier has a knife edge that both cuts theextraction filter and serves as an energy director for ultrasonicwelding to the base. Panel (d) shows the configuration of the filterafter ultrasonic welding. The knife edge melts during ultrasonic weldingand forms the weld bead. The thickness of the filter, the depth of therecess in the top carrier, and the depth of the weld determine theamount of filter compression.

FIG. 3( e) shows one example of an aperture pattern for the top and basecarriers for the membrane material. The pattern shown has an exposedmembrane surface area of approximately 47%.

FIGS. 3( f-g) illustrate two non-limiting examples of configurations forreagent reconstitution chambers in the cartridge.

FIG. 3( h) shows the restriction zone in the flow path positionedbetween the denature zone and the anneal/extend zone (the first andsecond reaction temperature controlled zones). This feature causes anincrease in the driving pressure as liquid traverses it. The pressuresignal can therefore be used to determine the location of the front andback of a liquid slug and for closed-loop fluidic control.

FIG. 4 depicts a method of conducting a nucleic acid detectionmeasurement in a cartridge of the invention.

FIG. 5( a) is a simplified schematic of a reader configured to interfacewith a cartridge of the invention.

FIG. 5( b) shows one embodiment of a reader according to the presentinvention.

FIGS. 6( a-b) show heating elements in the heating block of an exemplaryreader of the invention.

FIG. 6( c) shows one embodiment of a cartridge and the varioustemperature controlled zones within.

FIG. 7 shows a fluidic control manifold of the reader of the invention.

FIG. 8 shows a mini-column prototype.

FIG. 9 shows pressure traces for a typical purification of DNA from amodel organisms using the mini-column prototype and shows the pressurescreated during i) loading of samples in GuSCN lysis buffer; ii) washingof the column with clean GuSCN lysis buffer (buffer 1) and ethanol(buffer 2); iii) drying of the column with air flow; and iv) elution ofnucleic acid with low ionic strength elution buffer.

FIG. 10 is a graph demonstrating that, relative to untreated sputum, upto 50 times more DTT-treated sputum could be loaded on the mini-columnprototype while maintaining acceptable pressures.

FIG. 11 demonstrates that multiple types of nucleic acid, includinggenomic DNA, plasmid DNA, and total bacterial lysate (containing bothgenomic DNA and RNA) could be captured and eluted from the purificationmembrane.

FIGS. 12( a-b) provides PCR amplification results for nucleic acidsspiked into clean buffer, whole blood or a solution containing 1 ug/uLhumic and fulvic acids. One hundred (100) fg of DNA from B. anthraciswas spiked into PBS (buffer only), whole blood (Blood spike), or abuffer sample containing 1 ug/uL humic acid and fulvic acid (humicSpike).

FIG. 13 shows the CT values for real-time analysis of eluted productfrom the mini-column prototype using the lysis procedure described here.

FIG. 14 shows the final primer sequences used to amplify gene targets.

FIGS. 15( a-b) shows that addition of tRNA completely reverses theinhibitory effect of RT enzyme on PCR. Panel A shows the amplificationof a DNA target (FT) using our 16-plex primer mix and a one step RT andPCR protocol (all primers for DNA and RNA targets present during RTstep). Panel B shows the amplification of the same DNA target (FT) usingtwo step RT and PCR protocol (only the reverse primers for the RNAtargets were present during the RT step and remaining primers were addedafter completion of RT step.

FIG. 15( c) shows the results of an experiment using a model 6-plex PCRassay to examine the tradeoff between PCR cycle duration and the numberof PCR cycles that can be run in a 15 min amplification reaction.

FIG. 16( a) shows that for the BA-PA target, an annealing temperature of56° C. and a cycle dedicating 60% of cycle time to the anneal/extendstep gave optimal amplification when using a fast (20 sec.) overallcycle time. The graph also shows that these values provide goodrobustness to small changes in temperature or anneal/extend time.

FIG. 16( b)-(e) show that the optimal denaturation temperature for fastPCR cycles was between 95 to 97° C.

FIG. 17 shows an amplification test bed with heating elements to holdthe flow cell and to establish the temperatures zones in the PCRreaction zone of the cartridge.

FIG. 18 is a table of amplification efficiencies measured in the flowcell prototype for each of our 16 targets.

FIG. 19( a-d) show results for amplification of SA genomic DNA.

FIG. 20( a) shows the final probe sequences used to detect PCRamplicons.

FIG. 20( b) shows the sequences of PCR primers prepared by shifting theposition of one of the primers on the target sequence to shorten thelength of the amplicon and remove nucleotides involved in secondarystructure formation.

FIG. 21( a-b) show the effects of these strategies on signals for theVEE 5′UTR and NSP4 targets.

FIG. 22( a-b) demonstrate the performance of our optimized 16-plex ECLsandwich hybridization assays in the multi-well plate format and theobserved levels of cross-reactivity of each target for the differentcapture probes.

FIG. 23( a-b) shows ECL signals for measuring amplicons from a model6-plex panel (our 6 genetic targets for BA, FT and YP).

DETAILED DESCRIPTION

The invention, as well as additional objects, features and advantagesthereof, will be understood more fully from the following detaileddescription of certain preferred embodiments. Where the terms “measure”or “measurement” are used herein, they are understood to encompassquantitative and qualitative measurement, and encompasses measurementscarried out for a variety of purposes including, but not limited to,detecting the presence of a thing or property, measuring the amount of athing or property, and/or identifying a thing or property in a sample.Unless otherwise defined herein, scientific and technical terms used inconnection with the present invention shall have the meanings that arecommonly understood by those of ordinary skill in the art. Further,unless otherwise required by context, singular terms shall includepluralities and plural terms shall include the singular. The articles“a” and “an” are used herein to refer to one or to more than one (i.e.,to at least one) of the grammatical object of the article. By way ofexample, “an element” means one element or more than one element.

The present invention relates to assay cartridges, systems, and methodsof using the same, wherein the cartridge includes a fluidic network andone or more chambers and zones for conducting a multiplexed nucleic acidmeasurement on a biological fluid sample. In particular, the assaycartridge of the present invention is configured to conduct one or moresteps of a nucleic acid measurement, e.g., cell lysis, nucleic acidextraction, purification, amplification, and detection of PCR amplicons.The cartridge can be used in an assay system including a readerconfigured to interface with the cartridge. One embodiment of the readerincludes an enclosure, a cartridge tray and a mounting frame positionedwithin the enclosure to align the cartridge with one or more readercomponents, including but not limited to an optical detection assembly,an ampoule breaking mechanism, an electrode contact pin assembly, afluidic control manifold configured to enable fluid motion within thefluidic network of the cartridge, one or more optical sensors forfluidic control, and one or more heater assemblies.

The assay cartridge can include the necessary electronic componentsand/or active mechanical components for carrying out an assaymeasurement, e.g., one or more sources of electrical energy, ammeters,potentiometers, light detectors, temperature monitors or controllers,pumps, valves, etc. Preferably, some or all of the electronic and/oractive mechanical components are arranged within a separate reader. Thereader can also include the appropriate electrical, hydraulic, fluidicand/or optical connections to the assay cartridge for carrying out anassay on the assay cartridge. Using such an arrangement, the assaycartridge can be designed to be low cost and disposable while the reader(which holds the more expensive and complex components) is reusable. Apreferred assay procedure using the assay system of the inventioncomprises inserting the cartridge in the reader, which makes theappropriate electrical, fluidic and/or optical connections to thecartridge (making use of electrical, fluidic and/or optical connectorson the cartridge and reader), and conducting an assay in the cartridge.The sample is preferably introduced into the cartridge prior toinserting the cartridge in the reader. The assay can also involve addingone or more assay reagents to the cartridge, but in a preferredembodiment, one or more assay reagents are stored in the cartridge in adry and/or wet form.

The assay cartridge of the present invention preferably includes all therequired reagents and fluidic features to carry out all the stepsrequired to process and analyze a sample. FIG. 1( a) is a schematicrepresentation of the fluidic network and reagent storage and processingzones within the cartridge. The fluidic network within the cartridge caninclude a primary flow path (1) and one or more fluidic conduits (2),connecting the primary flow path to one or more chambers (3) forreagents and other materials/operations used and/or conducted in thecartridge during the conduct of an assay. The primary flow path includesan inlet (4), a purification zone (depicted in FIG. 1( a) between pointsA and B along the primary flow path), a reaction zone (shown in FIG. 1(a) between points B and C along the primary flow path), and a detectionzone (shown in FIG. 1( a) between points C and D along the primary flowpath). In addition, the primary flow path also includes one or more airvent ports (5). The fluidic conduits intersect the primary flow path andconnect a chamber to the primary flow path as well as each chamber to anadditional air vent port (6). The fluidic network is configured to metera volume of fluid in the primary flow path.

As shown in FIG. 1( a), the cartridge can include a plurality ofchambers (3), for example, a sample chamber (3 a), a mixing chamber (3b), one or more liquid and/or dried reagent chambers (3 c-f), and one ormore waste chambers (8 a-b). The chambers are connected to the primaryflow path via a plurality of fluidic conduits, so that a sampleintroduced into the sample inlet can be routed to a sample chamber, anda metered volume of sample can be sequentially delivered to andprocessed in one or more chambers/zones intersecting and/or positionedalong the primary flow path. The vent ports are positioned in thefluidic network in fluidic communication with the various chambers,purification, reaction, and detection zones (directly or through ventconduits) so as to allow the equilibration of fluid in the chambers withthe atmosphere or to allow for the directed movement of fluid into orout of a specified chamber/zone by the application of positive ornegative pressure.

In a specific embodiment, a fluidic conduit within the fluidic networkincludes a multi-conduit fluidic junction (11) as shown in FIG. 1( b)including (i) a first conduit (12) connecting the primary flow path anda chamber (3), and (ii) a second conduit (13) connecting the chamber tothe additional air vent port (6), wherein the first conduit is incommunication with an optical fluid sensor (7 a) at a position distalfrom the fluidic junction, i.e., the point at which the primary flowpath is intersected by the first conduit (represented in FIG. 1( b) aspoint E). The direction of fluid flow is shown by arrow (1 a). In oneembodiment, fluid is directed through the primary flow path (1) and whenthe fluid flow reaches optical sensor (7 a) (point F), i.e., the opticalsensor in communication with the first fluidic conduit of themulti-conduit fluidic junction (11), the fluid flow path is vented toatmospheric pressure by vent (5 a), stopping fluid flow at point F. Asvent (5 a) is opened, vent (5 b) remains closed. Once fluid flow atpoint F is stopped, vent (5 a) is closed and air is introduced by vent(5 b) to push fluid upstream in the primary flow path (1). This methodgenerates a metered volume of fluid wherein the volume is defined by thedistance between the intersection of the vent (5 b) and the primary flowpath, and the optical sensor in communication with the junction (pointF). The sample chamber fluidic junction is also in communication with asample chamber optical fluid sensor (7 a) at a position distal from thesample chamber fluidic junction and a metered volume of fluid traversingthe fluidic network is alternatively defined by the distance between thesample chamber fluidic junction and the distal position. As discussed inmore detail below, in this alternate embodiment, once the fluid front inthe primary flow path reaches an optical sensor in communication with amulti-conduit fluidic junction, the fluid front can be backflowed intothe chamber of the junction. The contents of the chamber can then bereintroduced into the primary flow path and directed in the forwarddirection along the primary flow path to a subsequent chamber/zone inthe cartridge. Hence, the volume of fluid metered in the fluid flow pathis defined by the geometry of the microfluidic channel

Each of the chambers within the cartridge interface with the primaryflow path via a multi-conduit fluidic junction as shown in FIG. 1( b).As described above, fluid can be directed along the primary flow path inthe forward or reverse direction, with the direction of fluid flow beingcontrolled by the vent ports positioned in the fluidic network. The ventports act as control ports that allow a reader to control the movementof fluid in the cartridge, e.g., by a combination of sealing one or moreports, opening one or more ports to atmospheric pressure, connecting oneor more ports to a source of positive pressure, and/or connecting one ormore ports to a source of negative pressure.

Likewise, if the chamber is a mixing chamber, the metered volume offluid is directed along the primary flow path into the chamber via thefirst fluidic conduit, where it can be mixed with one or more reagentsand subsequently redirected to the primary flow path. A mixing chambercan also be connected to one or more reagent chambers and a meteredvolume of reagent can be directed into the mixing chamber, before orafter a metered volume of sample is introduced to the mixing chamber.Hence, the primary flow path is intersected by a mixing chambermulti-conduit junction including (i) a first mixing chamber conduitconnecting the primary flow path and the mixing chamber, and (ii) asecond mixing chamber conduit connecting the mixing chamber to a mixingchamber vent port. In a preferred embodiment, the mixing chamber fluidicjunction is in communication with a mixing chamber optical sensor at aposition distal from the mixing chamber fluidic junction and the meteredvolume of fluid traversing the primary flow path is defined by thedistance between the mixing chamber junction and the distal position. Ina preferred embodiment, the primary flow path further comprises a seriesof Z-transitions at a position distal from the mixing chamber fluidicjunction to facilitate mixing of the sample and reagent(s) added to thesample.

The fluidic network meters a volume of reagent from a reagent chamber asdescribed above in reference to FIG. 1( b), i.e., the contents of thereagent chamber are released into the first conduit and flow into theprimary flow path until the reagent reaches an optical sensor incommunication with the multi-conduit fluidic junction connected to thereagent chamber. When the reagent fluid front reaches the opticalsensor, a vent in the flow path is opened to atmospheric pressure tostop the reagent fluid front at the optical sensor, the vent is closedand a secondary vent is opened to direct the metered volume of fluid toflow in the desired direction. In the embodiment shown in FIG. 1( b),the fluid front in the primary flow path reaches optical sensor (7 a)and is back-flowed into the chamber (3). Thereafter, the contents ofchamber (3) are reintroduced into the primary flow path and directed inthe forward direction along the primary flow path to a subsequentchamber/zone in the cartridge. The chamber can also include an overflowoptical sensor (7 b) and as described herein and illustrated in FIG. 1(a).

Vent ports are preferably apertures on the surface of the cartridge thatare in fluidic communication with fluidic chambers or conduits withinthe cartridge. In a laminated cartridge construction, the vent ports canbe provided, for example, by apertures in cover layers that seal againsta cartridge body to define planar fluidic networks or alternatively, bythrough-holes exposed on one surface of the cartridge body thatcommunicate with fluidic networks on the opposing side. The vent portscan also be used to introduce air into liquid streams passing throughthe fluidic conduits of the invention, for example, to segment the fluidstreams with slugs of air. The introduction of air can be used toprevent mixing of two liquid slugs passed sequentially through aconduit, to clear a liquid from a conduit and/or to enhance theefficiency of a wash step. Preferably, the vent ports are arranged in asingle row at a common location along the cartridge body's width. Suchan arrangement and configuration of the control points advantageouslyallows the interface between the reader and the cartridge to besimplified. For example, using such a preferred configuration allows thereader to make use of a single fluidic mating device for placing thecartridge into fluidic communication with the reader. Such aconfiguration also allows the motion control subsystem(s) to besimplified in that a single motor or actuation device can be used toactuate the fluidic mating device and move it into sealing engagementwith the cartridge body.

The fluidic conduits can be located at any position within the cartridgeand oriented at any angle. Advantageously, the fluidic channels arelocated, primarily, in planar networks, preferably located proximate tothe outside surfaces to allow for a multi-layered cartridge design thatuses, e.g., machined, die-cut, laser-cut and/or molded cartridge bodycomponents. Preferred conduit geometries include conduits withcross-sections that are circular, semi-circular, oval, square orrectangular in cross-section. The width is, preferably, similar to theheight so as to minimize the surface area for a particularcross-sectional area. Width and height can vary widely from nm to cmranges depending on the application, sample volume and cartridge design.Preferred ranges for the width and height are 0.05 to 10 mm, preferably,0.25 to 3 mm, most preferably 0.5 to 2 mm. Cartridges adapted to lowvolume samples such as blood from finger pricks can have small conduits,preferably having height/widths <1 mm, preferably between 0.25 to 1.0mm.

The fluidic channels preferably include “Z-transitions” to route thefluid flow path between planes in the cartridge. A conduit with such aZ-transition can comprise first, second, and third conduit segmentsarranged in sequence, the first and third conduit segments being locatedin different planar fluidic networks and a second conduit segmentconnecting the two fluidic networks and arranged at an angle to theother two segments. By way of example, Z-transitions route the fluidflow/path from fluidic conduits near the upper surface to fluid conduitsnear the bottom surface and vice versa. Z-transitions are advantageousin that they provide capillary breaks (as described below) and allow formore complicated fluidic networks than would be possible if the fluidicconduits were confined to one plane. Z-transitions can be used topassively control the flow of fluids and prevent mixing of fluidstreams. Certain embodiments of the invention employ “doubleZ-transitions,” that is conduits that comprise a first Z-transition thatdirects fluid flow from a first planar network to a second planarnetwork, a second Z-transition that redirects fluid flow back to thefirst planar network and a connecting segment in the second planarnetwork that connects the two Z-transitions. Such a double Z-transitioncan comprise first, second, third, fourth and fifth conduit segmentsarranged in series, the first and fifth segments located in a firstplanar fluidic network, the third segment located in a second planarfluidic network, the second and fourth segments located so as to directflow between the two planar networks. A double Z-transition can be usedto traverse a channel without interruption (“jumping over” a channel) orto cross another type of boundary.

The fluidic network can be formed within the cartridge in a number ofdifferent ways, dependent, in part, upon the materials chosen for thecartridge. Any known fabrication method appropriate to the cartridgebody material can be employed including, but not limited to,stereolithography, chemical/laser etching, integral molding (i.e.,channels are formed as the part is being molding during manufacturing),machining, lamination, etc. Such fabrication methods can be used aloneor in combination. In certain embodiments of the invention, thecartridge comprises a cartridge body and one or more cover layers matedto surfaces of the cartridge body so as to define one or more fluidicnetworks (preferably, planar fluidic networks) there between. Similarly,Z-transitions and/or ports can be selectively molded into, or machinedout of, the cartridge body at predetermined locations to form thefluidic connections between the channels on the upper and lowersurfaces.

One preferred embodiment of the cartridge can be fabricated using a“lamination” process whereby the cartridge body's functional surfacesare sealed using cover layers to form the fluidic network. For example,recesses (e.g., channels, grooves, wells, etc.) in one or more surfacesof the cartridge body provide what is referred to herein as “functionalsurfaces.” Sealing/mating of the functional surfaces to cover layersforms a fluidic network comprising fluidic components (e.g., conduits,chambers, etc.) at least some of which are defined in part by therecesses in the cartridge body and in part by a surface of a coverlayer. The cover layers are preferably comprised of plastic film such asmylar film. The cover layer can be coated with an adhesive to seal thecover layer against the cartridge layer. Other methods for mating thecover layer to the cartridge body will be known to the skilled artisan,e.g., the seal can be achieved by heat sealing, ultrasonic welding, RF(radio frequency) welding, by solvent welding (applying a solventbetween the components that softens or partially dissolves one or bothsurfaces), by use of an intervening adhesive layer (e.g., a double sidedadhesive tape, etc.). Advantageously, cartridge features that arecreated by patterned deposition (e.g., patterned deposition of electrodeor dielectric layers and/or patterned deposition of reagents to form dryreagent pills or to form binding domains with immobilized bindingreagents) are created on cover layers so as to take advantage ofautomation available to process plastic film in large sheets or rolls.

Recesses can be, for e.g., molded in, etched in or machined from thecartridge body. By analogy, fluidic components can also be defined, atleast in part, by recesses in a cover layer that is mated to a cartridgebody. Fluidic components can also be defined, at least in part, byregions cutout from gasket layers disposed between the cartridge bodyand cover layers. Apertures in the cartridge body and/or cover layerscan be used to provide for access ports to the fluidic network, e.g.,sample introduction ports, vent ports, reagent addition ports and thelike. Vent ports, preferably, allow the equilibration of fluid in thechambers with the atmosphere or to allow for the directed movement offluid into or out of a specified chamber by the application of positiveor negative pressure. In a preferred embodiment, fluid is moved in thefluidic network by applying positive or negative air pressure, withoutdirectly applying pressure on the fluid front. Vent ports, preferably,are designed to prevent the leakage of liquid samples or reagentsthrough the ports and can include aerosol-resistance filters, membraneor filter materials that permit air flow but act as barriers to aqueoussolutions (e.g., filter or membranes made from porous hydrophobicmaterials such as Gore-Tex®), and materials that are porous to air butseal when they come in contact with aqueous solutions (e.g., cellulosegum impregnated filters).

Preferred embodiments include a cartridge having a cartridge body with afirst side and a second, preferably opposing, side and one or more coverlayers mated to the first side to form a first fluidic network therebetween and one or more cover layers mated to the second side to form asecond fluidic network there between. Through-holes through thecartridge body (which can be formed by molding, etching, machining,etc.) can be used to link the first and second fluidic networks and toprovide Z-transitions. Additional fluidic complexity can be built into acartridge by employing a laminated cartridge body having multiplecartridge body layers and additional fluidic networks between theselayers; through-holes through the various cartridge body layers are usedto link the different fluidic networks.

A high degree of control over the movement of liquids in the cartridgesof the invention can be attained, without the introduction of activevalve elements in the cartridge, through the use of fluidic networkscomprising capillary breaks. “Capillary break,” as used herein, refersto a region in a fluid conduit that acts as a barrier to liquid movingthrough the conduit under capillary action or under the driving force ofa low pressure gradient below a threshold pressure. In preferredexamples of capillary breaks, application of a pressure above thethreshold pressure acts to push the fluid past the barrier. Capillarybreaks can be designed into fluid conduits by introducing, e.g., i) atransition, on a surface of a conduit, from a wettable surface to a lesswettable surface (e.g., as indicated by the contact angle for water);ii) a transition in conduit width from a region of narrow width thatpromotes capillary flow to a region of wider width; iii) a transition,on a surface of a conduit, in roughness; iv) a sharp angle or change indirection and/or v) a change in cross-sectional geometry. In anotherembodiment, a fluid conduit has a flexible wall/diaphragm that impingesinto the conduit and blocks flow driven by a pressure below a thresholdpressure. Application of a higher pressure forces the flexiblewall/diaphragm out of the flow path and lets fluid flow. In oneembodiment, the diaphragm is made of a material (e.g., Gore-Tex) thatallows gas to pass through but prevents the flow of liquid up to acertain pressure. Preferred capillary breaks involve a sharp angle orchange in direction in a fluid conduit.

In one embodiment of the invention, a liquid is introduced into achamber comprising an outlet conduit that includes a capillary break(preferably a Z-transition). The liquid enters the outlet conduit butstops at the Z-transition. A pressure gradient is then applied (e.g., byapplying positive pressure to the chamber or negative pressure to theother end of the conduit) which cause the liquid to flow past theZ-transition into the rest of the conduit.

The sample chamber (3 a) is adapted to receive a sample to be analyzedin the cartridge. The sample chamber includes a sample introduction portfor introducing sample into the chamber (with regard to the design ofthe sample introduction port, reference is made to U.S. Ser. No.10/744,726, filed Dec. 23, 2003, and FIGS. 35(a-b) and 47(a-b) andaccompanying text of U.S. Ser. No. 12/959,952, filed Dec. 3, 2010, thedisclosures of which are hereby incorporated herein by reference). Theport is preferably an opening in the cartridge that provides access tothe sample chamber. Alternatively, the port can be a membrane or septathrough which a sample can be injected into the sample chamber, e.g.,through the use of a needle or cannula. Preferably, the cartridge alsoincludes a sealable closure for sealing the sample introduction port andpreventing leakage of the sample and possible exposure of the userand/or associated instruments to biohazards. Preferably thesealing/capping mechanism utilizes a hinged configuration so that thesample chamber is easily accessed and sealed. In particularly preferredembodiments the sealing/capping mechanism incorporates a flexible hinge,e.g., rubber, plastic or the like. Most preferably, the sample chamberis adapted and configured to receive a modular detachable insert thatincludes a cap for sealing the sample chamber. Use of a modulardetachable insert within the sample chamber also allows for independentselection of materials for the main cartridge body. In an alternativeembodiment, sealing of the sample introduction port is achieved byapplying an adhesive tape to the port. The sample chamber can containdry reagents used in carrying out the assay that reconstitute onaddition of a liquid sample.

The sample chamber can also include a filter for, e.g., removingparticulate matter that can be present within the sample itself or thatcan be present as a result of using a swab or the like to introducesample into the sample chamber. A preferable embodiment can employ afilter that not only removes any particulate matter but that is alsodesigned to separate red blood cells (RBC) from blood plasma; e.g.,where the particular assay/assay format requires blood plasma as thesample. Such a filter can be an integral cross-flow filter, in-linefilter or the like. Preferably, the filter is arranged at or near theentrance of the sample conduit. As described above, the sample chamberis connected to the primary flow path by a sample chamber multi-conduitfluidic junction including (i) a first sample chamber conduit connectingthe primary flow path and the sample chamber; and (ii) a second samplechamber conduit connecting the sample chamber to a sample chamber airvent port via an overflow waste chamber. A liquid sample is added to thesample chamber and the operator closes the cap. After sample addition,the cartridge meters a pre-defined volume of sample for processing.After the sample volume is metered, the fluid slug is moved into amixing chamber (3 b), where it is combined with a metered volume ofreagent stored in reagent chamber (3 c).

The reagent chambers are adapted to hold liquid reagents used duringsample processing (with regard to the design of reagent chambers in acartridge, reference is made to U.S. Ser. Nos. 10/744,726, filed Dec.23, 2003, and 12/959,952, filed Dec. 3, 2010, the disclosures of whichare hereby incorporated herein by reference). Liquid reagents that canbe held in a reagent chamber include buffers, assay diluents, solutionscontaining binding reagents (e.g., proteins, receptors, ligands,haptens, antibodies, antigens, nucleic acids and the like), solutionscontaining enzymes and/or enzyme substrates, solutions containingcontrol reagents, ECL read buffers containing ECL co-reactants (e.g.,tertiary amines such as piperazine-N,N′-bis(2-ethanesulfonic acid) andtripropylamine), wash solutions, anti-foam agents, extraction reagents(e.g., solutions containing detergents, acids, bases, etc.) and thelike. A cartridge can have one, two or more reagent chambers depending,for e.g., on the number of reagents required for sample processing inthe cartridge and/or by the assay format. The reagent chamber isconnected to the primary flow path as described above and as illustratedin FIG. 1( b). Optionally, a filter element is placed before or in thereagent conduit, e.g., if the reagent solution is expected to containparticles that can clog the cartridge fluidics or otherwise negativelyaffect assay performance.

Preferably, where an assay requires the use of liquid reagents, some orall of these liquid reagents are stored in liquid form in reagentchambers so as to minimize the number and complexity of the operationsthat must be carried out by a user or reader. In one preferredembodiment the reagent chamber(s) can be filled with the requisite assayreagent(s) at the time of cartridge manufacture and subsequently sealed.When used to store liquid reagents, the reagent chambers should bedesigned to prevent leakage and/or evaporative loss of the reagents fromthe chambers during storage. In a preferred embodiment, an assay reagentrelease mechanism would be incorporated within the reader for releasingthe assay reagent from the reagent cartridge. The assay reagent releasemechanism is preferably adapted and configured to engage the reagentchamber and release/recover its contents.

The reagent chamber is a container such as an ampoule (e.g., glass,plastic, or the like), a pouch (e.g., plastic, metal foil, plastic/metalfoil laminates, rubber, or the like), a blister pack, a syringe, or thelike, or any other container that can be filled with fluid, sealed anddropped into the cartridge for subsequent fluid delivery. Preferredmaterials include glass, plastics with good water vapor barrierproperties (e.g., cyclic olefin copolymers such as copolymers ofethylene and norbornene, nylon 6, polyethyelene naphthalate,polyvinylidene chloride and polychlorotrifluoro-ethylene) and metalfoil/plastic laminates because of their chemical inertness and theirresistance to evaporative losses; other suitable materials will beapparent to the skilled practitioner. Ampoules preferably comprise amaterial that can be made to shatter or break on impact such as glass orhard plastic. Embodiments incorporating breakable ampoules preferablyalso include filters to ensure that substantially all of the fragmentsthat can result upon rupturing the ampoules are not permitted to enterthe fluidic network and possibly obstruct/block fluid flow. The reagentchambers include an outlet port (or drain) for transferring reagent outof the reagent chamber. The outlet can include a filter element forpreventing glass shards from entering the cartridge fluidics.

Optionally, ampoules are used as reagent chambers and the ampoules restin an ampoule cradle adapted to receive a cylindrical ampoule (withregard to the design of an ampoule cradle, reference is made to FIG. 36and the accompanying text of U.S. Ser. No. 12/959,952, filed Dec. 3,2010, the disclosure of which are hereby incorporated herein byreference). The ampoule cradle, i.e., a reagent chamber, includes sidewalls and a plurality of support brackets protruding from the sidewalls, and the support brackets are configured to provide a multi-pointcradle support for a cylindrical ampoule. The reagent chamber caninclude three, four or more support brackets, protruding from the sidewalls, at least one bracket being present on each side of the chamber.The brackets are, preferably, sloped inward such that the width of thereagent chamber becomes narrower with increased depth in the well (inwhich case, the side walls themselves do not need to be sloped). In oneembodiment, the side walls of the chamber are also sloped. The bracketsprovide a multi-point cradle support for the ampoules (e.g., a three orfour point cradle design) that allows for significant tolerance in thelength of the ampoules. The surface of the supports that contact andsupport the ampoule can be slanted (as shown) or flat. The width of thebrackets (i.e., the dimension along the length of the chamber) can benarrow (e.g., <5 mm or less than 2 mm) to focus forces on relativelysmall regions of the ampoule during ampoule breaking.

An important consideration for cartridge based assay systems relates tolong term storage of the cartridge prior to use; i.e., “shelf life” ofthe cartridge. Certain assay reagents (especially biological reagentsand/or binding reagents such as enzymes, enzyme substrates, antibodies,proteins, receptors, ligands, haptens, antigens, nucleic acids and thelike), when dissolved in a liquid medium require special handling andstorage in order to improve their shelf life. In certain instances, evenif the assay reagents dissolved in liquid media are handled and storedin strict compliance with the special handling and storage requirementstheir shelf life is impracticably short. Furthermore, the need toobserve special handling and storage requirements adds to the complexityand cost of the cartridge based system employing such reagents. Thespecial handling and storage requirements can be substantially reduced,if not eliminated, and the complexity and cost of the system can beminimized by using more stable dry, or dehydrated, forms of the assayreagents. The use of dry reagents can also simplify mixing operationsand reduce the volume and weight of a cartridge. Reagents that can beincluded in dry form include biological reagents, binding reagents, pHbuffers, detergents, anti-foam agents, extraction reagents, blockingagents, and the like. The dry reagent can also include excipients usedto stabilize the dry reagents such as sugars (e.g., sucrose ortrehalose). For assays that employ acidic or basic samples (e.g.,samples that are inherently acidic/basic and/or samples that areextracted or otherwise treated with an acidic/basic reagent), a dryreagent can include a neutralizing reagent (e.g., an acid, base, or a pHbuffer).

Dry reagents can be employed in a cartridge in a number of ways. Dryreagents can be stored in a reagent chamber that is filled prior to useby a user or by a reader apparatus. Similarly, dry reagents can bestored in other fluidic components such as within fluidic conduits,along the primary flow path, or in chambers, most preferably within thepurification, reaction, and detection zones. In one embodiment, reagentsare provided in the form of a dry pill and are retained in reagentreconstitution chambers. Reagent reconstitution chambers are in fluidiccommunication with the primary flow path, allowing fluid to enter thechamber and dissolve the dried reagent pill. In one embodiment, areagent reconstitution chamber has a fluid inlet at the bottom of thechamber (or below the location of the pill) and a vent located at thetop of the chamber (or above the location of the pill). The chamberholds a pill between the inlet and the vent but, preferably, providesfluid paths around the pill to allow for facile introduction of fluidinto the chamber without pressure build-up. The pill may be held betweenthe inlet and the vent by pill retaining features defined by the chamberwalls. The pill retaining feature can be a cradle defined by slopingbrackets (as described above in the context of features for holdingampoules). Alternatively, the walls of the chamber are shaped to conformto the shape of the pill and, preferably, taper down towards the bottomof the chamber to provide a seat that firmly holds the pill throughmulti-point contacts. In this case, fluidic paths around the bead can beprovided by distorting the shape of the walls so that they are notperfectly conformal with the bead or by introducing lobes that breakcontact with the bead at defined locations. In one embodiment, the beadis spherical or cylindrical and the pill seat is defined by taperedwalls that are oblong in cross-section or that are generally circular incross-section except for the presence of lobes that provide fluid pathsaround the bead. In one preferred embodiment, the internal diameter nearthe top of the chamber is at least 0.1″ or 0.125″ or about 0.15″ topermit bubbles formed in the chamber to burst prior to entering thevent. In one specific example, the pill is retained through the use of achamber with an oblong or tri-lobed wall design, shown in FIGS. 3 f and3 g, respectively.

In operation, a fluid slug is introduced into the reagent reconstitutionchamber through the inlet port, while air in the chamber exists throughthe vent port. The fluid slug volume is selected to reach and,preferably, completely immerse the pill, but not reach the vent port.The dry pill is dissolved in the fluid slug. The fluid slug, nowcontaining the dry reagents, is then removed back through the inlet.Optionally, reconstitution and mixing of the reagent in the slug can beaided by repeatedly pulling the slug in and out of the chamber throughthe inlet or, after introduction of the slug into the chamber, byintroducing air through the inlet to form bubbles that pass through thefluid in the chamber and out the vent port.

In an alternate embodiment, a fluid slug is introduced into the chamberto dissolve the dry pill and is then removed through the vent port.

Dry reagents can be inserted during the manufacture of a cartridge bydepositing the dry reagents in the appropriate fluidic component, e.g.,by depositing the reagent in the form of a powder or pellet or byincorporating the dry reagent in a screen printed ink. Alternatively,the reagents can be inserted in solution and then dried to remove thesolvent. In one preferred embodiment, dried reagents can be formed upona substrate by depositing solutions containing the reagents in one ormore predefined locations and subsequently drying the reagents to form adried reagent pill under conditions such that on addition of a liquidsample or an appropriate solvent, the dry reagent dissolves intosolution. The term “pill” is used herein to refer generally to an amountof a dry, but redissolvable, reagent on a substrate and not to connoteany specific three dimensional shape. A pill can be attached to asubstrate or free standing. The location of a pill on a substrate isreferred to herein as a “pill zone.” The substrate is preferably acomponent of the cartridge, e.g., cartridge body, chamber, cover layer,electrode array, etc. Suitable locations for the pill zone include thesample chamber, reagent chamber, primary flow path, fluidic conduits,and/or reconstitution chambers, so that liquid reagents and samples pickup the dry reagent prior to their introduction to the detectionchambers. Alternatively or additionally, reagent pills can be locatedwithin the detection zone. In the preferred embodiment, a reagentchamber holds a liquid reagent in an ampoule and a dry reagent pill, sothat the dry reagent is reconstituted upon rupture of the ampoule.

A pill zone in which dried reagents are deposited can be prescribed by aboundary which confines the volume of a deposited solution (and,therefore, the dried reagent left after allowing the solution to dry) toa specific region of a substrate. According to one embodiment of theinvention, a cartridge comprises a pill zone that is bounded by aboundary surface, the boundary surface being raised or lowered(preferably, raised) and/or of different hydrophobicity (preferably,more hydrophobic) than the pill zone. Preferably, the boundary surfaceis higher, relative to the substrate surface within the pill zone, by0.5-200 micrometers, or more preferably by 2-30 micrometers, or mostpreferably by 8-12 micrometers. Even more preferably, the boundarysurface has a sharply defined edge (i.e., providing a steep boundarywall and/or a sharp angle at the interface between the pill zone and theboundary). Preferably, the pill zone surface has a contact angle forwater 10 degrees less than the boundary surface, preferably 15 degreesless, more preferably 20 degrees less, more preferably 30 degrees less,even more preferably 40 degrees less, and most preferred 50 degreesless.

In one preferred embodiment the pill zone is defined by a depression cutor molded into the substrate. In another embodiment, the boundarysurface around a pill zone is defined by a boundary material applied onthe substrate. In one example, the pill zone is defined by a cutout in afilm or gasket applied to the substrate, preferably a cutout in a filmof adhesive tape. In another preferred embodiment the boundary can bephysically defined by applying a coating in a manner which defines theboundary of the pill zone using, e.g., established techniques forforming patterned coatings such as photolithography, patterneddeposition, screen printing, etc. In one example, a patterned dielectriccoating can be screen-printed onto the surface of a substrate material,the pattern including apertures, the boundaries of which define the pillzone. The reagent can then be dispensed onto the substrate within thepill zone boundary and thereafter dried to form the dried reagent pill.

The waste chambers are adapted to hold excess or waste liquid (withregard to the design of waste chambers, reference is made to U.S. Ser.Nos. 10/744,726, filed Dec. 23, 2003, and 12/959,952, filed Dec. 3,2010, the disclosures of which are hereby incorporated herein byreference). Sizing of the waste chambers is preferably done inaccordance with the anticipated volume of sample and liquid reagentsthat will be used in the assay. Another sizing-related factor for thewaste chambers that is preferably taken into account relates to thepotential for waste fluids, as they enter the waste chamber to foam orbubble. In such instances, where foaming or bubbling is anticipated, thewaste chamber volume could be increased sufficiently to avoid any issuesthat can arise from such foaming or bubbling.

As described above, waste chambers are linked to the primary flow pathvia a waste chamber conduit and to a vent port (e.g., through a ventconduit). The waste chamber is configured to allow liquid waste to bedelivered to the waste chamber through the waste chamber conduit and,preferably, for air that is included in the waste stream to escapethrough a waste chamber vent port. Optionally, the waste chamberscontain a water absorbing material, such as a sponge, that retains wastefluid and prevents leakage of the waste fluid on disposal of acartridge. A factor that is preferably considered when designing theconfiguration and arrangement of the waste chambers relates toeliminating or substantially reducing the possibility that fluid fromthe waste chamber can flow back (“back-flow”) into the cartridge'sfluidic network.

As described above, sample is added via a sample inlet and stored in thesample chamber. A metered volume of sample is delivered to the mixingchamber into which an additional reagent can be added via a reagentchamber. In a preferred embodiment, a metered volume of reagent is firstdelivered to the mixing chamber, followed by the addition of a meteredvolume of sample from the sample chamber. Mixing is facilitated byaerating the contents of the mixing chamber by opening and closing oneor more vent ports directly or indirectly connected to the mixingchamber. In a preferred embodiment, the mixing chamber includes anantifoam reagent, for example, SE-15, Antifoam 204, Antifoam A, AntifoamB, Antifoam C, Antifoam Y-30, and combinations thereof (available fromSigma-Aldrich Corp., St. Louis, Mo., www.sigmaaldrich.com). The airwhich is pumped through the fluid in the mixing chamber displaces anamount of liquid. The mixing chamber is preferably sized and shaped toprevent the escape of liquid into the air vent conduit during aerationand to accommodate fluid flow into and out of the mixing chamber.

As shown in FIG. 1( a), after mixing, the sample is delivered from themixing chamber to the purification zone for purifying target material ina sample, e.g., nucleic acids, from potential interferents. The basicdesign is amenable to use with a variety of known approaches forcapturing, washing and eluting nucleic acids including approaches thatgenerally target all nucleic acids in a sample (such as binding to glassmembranes) as well as approaches that target specific sequences (such asbinding to membranes or other solid supports that present specificcapture sequences). The purification zone can include a waste chamber (8a), one or more purification reagent chambers (3 d-e), and an integratedpurification membrane (9). In a preferred embodiment, the purificationzone comprises, from a proximal to a distal end, a purificationmulti-conduit fluidic junction including (i) (a) a first purificationreagent chamber conduit connecting the primary flow path and thepurification reagent chamber; and (b) a second purification reagentchamber conduit connecting the purification reagent chamber and apurification reagent chamber air vent port; (ii) an integratedpurification membrane positioned in the primary flow path of thepurification zone; and (iii) a waste multi-conduit fluidic junctionincluding (a) a first waste chamber conduit connecting the primary flowpath and the waste chamber; and (b) a second waste chamber conduitconnecting the waste chamber and a waste chamber air vent port. Thepurification membrane can be positioned on a support fit within theprimary flow path and the membrane can be compressed prior to cartridgeassembly. In a specific embodiment, the membrane comprises a glass fibermembrane.

In operation, a solution containing material to be purified is passedthrough the membrane under conditions in which the material is bound tothe membrane. The remaining solution is collected in the waste chamber.One or more wash buffers are passed through the membrane to removecontaminants and the flow-through is collected in the waste chamber. Thewashing step with each buffer may be repeated one or more times toimprove wash quality. Optionally, the membrane is dried by passing airthrough it, prior to elution of purified material from the membrane. Thepurified material is then eluted from the membrane by passing an elutionbuffer through the membrane.

Some nucleic acid purification methodologies benefit from heating of thepurification matrix during elution of nucleic acids and, optionally,during washing of the matrix prior to elution of the nucleic acids. Oneembodiment of the purification zone includes i) a pre-heating zone thatheats the primary flow path to the membrane and/or a ii) a membraneheating zone that surrounds the membrane carrier and heats theintegrated membrane. In an more specific embodiment, during the elutionof purified material from the membrane (and, optionally, during washingand drying of the membrane), the fluid flowing into the membrane and/orthe membrane itself are heated to about 60-80° C., and preferably about70° C.

The eluate is then directed along the primary flow path to the reactionzone. Reagents required for the conduct of a reaction in the reactionzone can be stored in one or more reagent chambers within the cartridgeand/or as dried pills stored within the primary flow path in thereaction zone and/or in one or more reconstitution chambers (10 a and 10d). In one embodiment of the invention, a cartridge has one or morereconstitution chambers that are empty or contain only dried reagents.Prior to conducting an assay, the user or reader dispenses liquidreagents into these chambers (e.g., through reagent vent ports orthrough reagent introduction ports similar to the sample introductionport described above) which, optionally, reconstitute any dried reagentpresent in the chambers; the reagents are thus prepared for use in theassay. In a preferred embodiment, all reagents are stored in liquidand/or dried form in the cartridge and prior to conducting an assay or astep of an assay, the reader breaks the reagent ampoule(s) to dispensereagent and/or the fluid in the fluidic network reconstitutes driedreagents in the flow path. Sealable closures can be used to preventleakage of the reagents after their addition. The reaction zone alsoincludes a first reaction temperature controlled zone (10 b) and asecond reaction temperature controlled zone (10 c) and the fluidicnetwork is configured to shuttle a volume of fluid between the first andsecond reaction temperature controlled zones during a reaction conductedin the reaction zone.

The primary flow path leads from the reaction zone outlet to thedetection zone. The detection zone is intersected by a detection reagentmulti-conduit junction connecting (i) the primary flow path and one ormore detection reagent chambers; and (ii) one or more detection reagentchambers and one or more detection reagent air vent ports. The detectionzone is adapted for carrying out a physical measurement on the sample.In a preferred embodiment, the detection zone is configured to measureluminescence and in this regard, reference is made to U.S. Ser. No.10/744,726, filed Dec. 23, 2003, and Ser. No. 12/959,952, filed Dec. 3,2010, the disclosures of which are incorporated herein by reference. Ifthe measurement requires illumination or optical observation of thesample (e.g., as in measurements of light absorbance, photoluminescence,reflectance, chemiluminescence, electrochemiluminescence, lightscattering and the like) the detection zone should have at least onetransparent wall arranged so as to allow the illumination and/orobservation. When employed in solid phase binding assays, the detectionzone preferably comprises a surface (preferably, a wall of the chamber)that has one or more binding reagents (e.g., antibodies, proteins,receptors, ligands, haptens, nucleic acids, etc.) immobilized thereon(preferably, an array of immobilized binding reagents, most preferablyan array of immobilized antibodies and/or nucleic acids). In anespecially preferred embodiment, the detection zone is anelectrochemiluminescence detection zone, most preferably having one ormore binding reagents immobilized on one or more electrodes. In onepreferred embodiment, the cartridge includes a working electrode havingan array of binding reagents immobilized thereon. In another preferredembodiment, the cartridge comprises an array of independentlycontrollable working electrodes each having a binding reagentimmobilized thereon. In cartridges employing arrays of binding reagents,at least two elements of the array comprise binding reagents that differin specificity for analytes of interest. Depending on the detectiontechnology employed in the cartridge, the detection zone can alsoinclude a detection temperature controlled region. In a preferredembodiment, the detection zone is an electrochemiluminescence detectionzone and the detection zone includes a detection temperature controlledregion designed to maintain the temperature of the detection zonebetween about 20-40° C., preferably 20-35° C., and most preferably25-35° C.

Depending on the application, manufacturing approach, sample size, etc.,the primary flow path dimensions in the detection zone can range fromnanometers to tens of centimeters and the volume from picoliters tomilliliters. Certain preferred embodiments have widths that can rangefrom 0.05-20 mm, more preferably, 1-5 mm and heights (preferably, lessthan or equal to the width so as to increase, for a given volume, thesurface area of the bottom of the detection zone, especially when thissurface is used to immobilize binding reagents) that range from 0.01-20mm, more preferably, 0.05-0.2 mm. Preferably, the height is less than orequal to the width. Preferably, the detection zone is designed toaccommodate sample volumes between 0.1-1000 uL, more preferably, 1-200uL, more preferably, 2-50 uL, most preferably, 5-25 uL. The primary flowpath in the detection zone preferably has a width greater than or equalto the height.

A cartridge can comprise one or more detection regions within thedetection zone. Cartridges comprising multiple detection regions cancomprise separate fluidic systems for each detection region (e.g.,multiple sample chambers and/or reagent chambers and associated fluidicconduits) so that assays on multiple samples can be carried out inparallel. In certain preferred embodiments, multiple detection regionsare linked to a single sample chamber and can share the use of otherfluidic components such as reagent chambers, waste chambers and thelike. In these embodiments, the two detection regions can be used tocarry out different sets of assays, thus increasing the number ofmeasurements that can be carried out on a sample relative to a cartridgewith one detection region.

In an alternate embodiment employing a plurality of detection regions,one or more of a plurality of detection regions is used ascontrol/calibration region for measuring assay control/calibrationsamples. In one such embodiment, a first and a second detection regionare each configured to carry out a panel of one or more assays for oneor more analytes. One detection region (the test region) is used toanalyze a sample. The other detection region (the control region) isused to analyze a spiked sample having a predetermined additional amountof the one or more of the analytes of interest (this predeterminedadditional amount, preferably, being provided by passing the samplethrough a reagent pill zone comprising the additional amounts). Thechange in signal between the two regions allows for the calculation ofthe responsiveness of the signal to changes in analyte and can be usedto calibrate the system and/or to determine if the cartridge isfunctioning properly. In another embodiment employing a control region,the control region is not used to analyze the sample or a derivativethereof, but is used to measure analyte in a separate control orcalibrator matrix. The signal in the control region can be used fordetermining background signals (by using a matrix with no analyte), forcalibrating the instrument (by using a calibrator matrix with apredetermined amount of analyte to determine calibration parameters) orto determine if the cartridge is functioning properly (by using acontrol matrix with a predetermined amount of analyte and determining ifthe signal falls within a predetermined acceptable range).

A preferred embodiment of the invention is depicted in FIG. 2( a). Thecartridge depicted in FIG. 2( a) includes the fluidic network and aplurality of chambers, as described above and illustrated in FIGS. 1(a-b). The cartridge is configured to conduct multiplexed nucleic acidmeasurements and optionally sample processing, including one or moresteps of nucleic acid extraction, purification, amplification, anddetection of PCR amplicons. In a preferred embodiment, the cartridge isconfigured to conduct lysis, purification, and elution steps inapproximately 15 minutes or less, reverse transcription in approximately5 minutes or less, amplification in approximately 15 minutes or less,detection reagent binding in approximately 5 minutes or less, anddetection in about 5 minutes or less, for a total analysis time of about45 minutes or less. The cartridge includes a fluidic network such asthat described above, including a primary flow path and one or morefluidic conduits, as well as a plurality of chambers for reagents andother materials and/or operations used and/or conducted in the cartridgeduring the conduct of an assay. The primary flow path includes a sampleinlet (21), a purification zone (22), a PCR reaction zone (23), and adetection zone (24). In a preferred embodiment, all amplicons are movedfrom the detection zone into the waste chamber (30) once detected. Inaddition, the primary flow path also includes one or more air vent ports(25). Like the cartridge embodied in FIGS. 1( a-b), the fluidic conduitsof the cartridge depicted in FIG. 2( a) intersect the primary flow pathconnecting the chambers to the primary flow path, as well as one or morechambers to an additional air vent port (not shown) and the fluidicnetwork is configured to meter a volume of fluid in the fluidic networkwithin the cartridge. As shown in FIG. 2( a), the cartridge includes aplurality of reagent chambers (26), a sample chamber (27), a mixingchamber (28), waste chambers (29 and 30), and a plurality ofreconstitution chambers (31).

As described above in reference to FIGS. 1( a)-(b), as shown in FIGS. 2(b)-(c), vent ports are preferably apertures on the surface of thecartridge that are in fluidic communication with fluidic chambers orconduits within the cartridge. The vent ports act as control ports thatallow the reader to control the movement of fluid in the cartridge,e.g., by a combination of sealing one or more ports, opening one or moreports to atmospheric pressure, connecting one or more ports to a sourceof positive pressure and/or connecting one or more ports to a source ofnegative pressure. As shown in FIG. 2( b), vent ports are arranged in arow at a common location along the cartridge body's width. Such anarrangement and configuration of the control points advantageouslyallows the interface between the reader and the cartridge to besimplified. Manifold interface ports are preferably located in a row(s)on the periphery of the cartridge along both sides as shown in FIGS. 2(b) (25 a and 25 b).

FIG. 2( c) is a cross-sectional view of the manifold interface portshown in FIG. 2( b) (25 c), which depicts an aerosol barrierincorporated into the cartridge at the point where the manifold mateswith the cartridge. The aerosol filter minimizes contamination byaerosols that could be generated during analysis. In one embodiment, theaerosol barrier achieves greater than 95% filter efficiency, andpreferably greater than 99% filter efficiency, down to less than 0.75um, and preferably less than 0.50 um. In one embodiment, the aerosolbarrier comprises a 10 um pore size filter available, e.g., from Porex.Preferably, the aerosol barrier is built into the consumable rather thanthe reader so that the manifold interface of the reader does not becomecontaminated.

A detailed flow diagram of the operation of the cartridge depicted inFIG. 2( a) is provided in FIG. 3( a). A liquid sample is introduced tothe sample inlet which is fluidically connected along the primary flowpath to the sample chamber. The cap on the sample inlet is sealed. Aftersample addition, the cartridge meters a volume of lysis buffer to themixing chamber (lysis chamber), and the cartridge subsequently meters avolume of sample to the mixing chamber. Mixing of the contents of themixing chamber is facilitated by aerating the contents of the mixingchamber via one or more of the vent ports connected directly and/orindirectly to the mixing chamber. In addition, mixing can be furtherfacilitated by the addition of a series of Z-transitions in the primaryflow path at a position distal to the mixing chamber fluidic junction,as shown in FIG. 3( b) (and preferably at a position following position7 a in FIG. 1( b)). The solution in the lysis chamber (32) is movedthrough the series of Z-transitions (vertical sections (33)) to promotemixing. As described above in reference to FIG. 1( b), optical sensorsthat monitor the fluidic channels on the fluidic network are used bothfor metering and mixing operations. The lysis buffer includesglutathione isothiocyanate (5 M), NaCl (300 mM), Tris-HCl, pH 7.4 (60mM), 1% Triton X-100, and optionally an antifoaming reagent. In apreferred embodiment, the mixing chamber includes a dried pill ofantifoam reagent prior to fluid addition to the chamber. The chaotropicsalt glutathione isothiocyanate lyses gram negative and, to a lesserdegree, gram positive bacteria that can be present in the sample, and italso denatures proteins in the sample, including nucleases.

Once the sample is lysed, it is re-directed to the primary flow path andmoved to the purification zone of the cartridge. The purification zoneincludes a waste chamber (29), one or more purification reagent chambers(26), and an integrated purification membrane (not shown). In apreferred embodiment, the purification zone comprises, from a proximalto a distal end, a purification multi-conduit fluidic junction including(a) a first purification reagent chamber conduit connecting the primaryflow path and the purification reagent chamber; and (b) a secondpurification reagent chamber conduit connecting the purification reagentchamber and a purification reagent chamber air vent port; (ii) anintegrated purification membrane positioned in the primary flow path ofthe purification zone; and (iii) a waste multi-conduit fluidic junctionincluding (a) a first waste chamber conduit connecting the primary flowpath and the waste chamber; and (b) a second waste chamber conduitconnecting the waste chamber and a waste chamber air vent port. In aparticularly preferred embodiment, the purification zone furthercomprises a pre-heating region (not shown) preceding the integratedpurification membrane and configured to heat the elution buffer tomaximize recovery of nucleic acids from the membrane. Preferably, thepre-heating region is in communication with one or more heating elements(or blocks) in the accompanying cartridge reader to heat the fluidwithin the pre-heating region to between 60 to 80° C., more preferablybetween about 65 to 75° C., and most preferably about 70° C.

As described above, the purification membrane, e.g., a glass fibermembrane, can be positioned on a support frit within the primary flowpath and the membrane can be compressed prior to cartridge assembly. Thegeometry of the primary flow path in the purification zone is preferablyconfigured to provide uniform fluid flow across the diameter of themembrane. In a preferred embodiment, the primary flow path in thepurification zone is configured to provide a fluid flow path with a highaspect ratio to ensure a uniform flow with a relatively low retentionvolume. This facilitates the efficient capture of nucleic acids on themembrane. In a preferred embodiment, the glass membrane is cut andassembled in situ in a single step of the manufacturing process of thecartridge. As shown in FIGS. 3( c-d), the resulting design is composedof top (34) and base (35) plastic carriers with the glass membranematerial (36) sandwiched in between. The knife edge (37) on the topcarrier cuts through the membrane material and then it is welded to thebottom carrier with the application of ultrasonic energy. Panel (c)shows the configuration of the filter after ultrasonic welding. Theknife edge (37) melts during ultrasonic welding and forms the weld bead.The thickness of the filter, the depth of the recess in the top carrier,and the depth of the weld determine the amount of filter compression.This approach minimizes handling of the membrane material and itfacilitates reproducible pre-compression of the membrane.

The aperture design on the base plastic carrier supporting the membranematerial can be optimized to increase the exposed surface area of themembrane material. A non-limiting example of an aperture design for thebase plastic carrier is depicted in FIG. 3( e). This design features asupport pattern (38) which is cross-shaped in the non-limitingembodiment shown in FIG. 3( e). The design shown optimizes the exposedmembrane surface area, thereby significantly reducing the pressure dropthat occurs as fluid is passed through the membrane. Additionalparameters can be adjusted to maximize nucleic acid recovery whilemaintaining a reasonable pressure drop across the filter, e.g., lessthan about 15 psi and preferably less than about 10 psi regardless ofthe fluid matrix. Such additional parameters include but are not limitedto weld depth, membrane diameter and pre-compression, and lysis bufferformulation. It is preferable to minimize the extraction volume in thepurification zone to facilitate rapid thermocycling and to provide acompact cartridge design. In one embodiment, the retention volume of themembrane less than 10 uL, preferably less than 5 uL, and most preferablyless than 2 uL. A volume of lysis buffer is added to the membrane andthe eluate is collected in the waste chamber. The membrane is washed bya wash cycle which includes the addition of wash buffers, preferablyincluding ethanol (most preferably 70% ethanol/water), to the membraneto remove contaminants, elution buffer is added (preferably 10 mM Tris1.0 mM, pH 7.5, including 1 mM EDTA), and the purified sample isdirected along the primary flow path to the PCR reaction zone.

In a preferred embodiment, the reaction zone is substantially adhesivefree and/or free of seams in order to reduce bubble formation. Reagentsrequired for the conduct of a reaction in the reaction zone can bestored in one or more reagent chambers within the cartridge and/or asdried pills stored in the primary flow path and/or in one or morereconstitution chambers fluidically connected to the primary flow pathin the reaction zone. Lyophilized pills containing the appropriatereagents can be stored in the reconstitution chambers and in oneembodiment, each chamber is includes a reagent used in a specific stepof the procedure carried out in the PCR reaction zone. In one specificexample, the pill is retained through the use of a chamber with anoblong or tri-lobed wall design, shown in FIGS. 3 f and 3 g,respectively.

In a specific embodiment, the cartridge includes a plurality ofreconstitution chambers: (a) the first chamber houses the pillcontaining the reagents for reverse transcription including the firststrand primers, Superscript-3 (reverse transcriptase), dNTP's, and otherreagents necessary for cDNA formation; (b) the next chamber houses thepill containing reagents for PCR amplification, including dNTP's,primers, and Taq polymerase; (c) a third chamber can include additionalprimers, if a specific application requires a nested PCR amplificationprotocol; (d) a fourth chamber houses lyophilized EDTA and salts toinhibit Taq polymerase and to increase the ionic strength of the fluidsample, preparing it for the final denature step after PCR amplificationis complete; and (e) a fifth reconstitution chamber holds the pill thatcontains the detection probes which is reconstituted after the sample isdenatured, just before presentation to the capture array. The reagentsin the first chamber are reconstituted and added to the primary flowpath with the purified sample, where fluid is directed to the reactionzone to enable cDNA synthesis. In a preferred embodiment, the reactionzone is maintained at about 47° C. during cDNA synthesis. The reagentsin the second chamber are then reconstituted and added to the fluid inthe primary flow path. An important step in genomic amplification is theinitial denature during which the long pieces of duplex DNA are meltedapart, exposing the primer binding sequences and allowing the primers tobind before elongation by Taq polymerase. In a preferred embodiment,double stranded genomic DNA is denatured for about 90 seconds beforecycling. Upon completion of this step the liquid sample containing thesingle stranded genomic material is moved from the first reactiontemperature controlled zone (maintained at approximately 96° C.) to thesecond reaction temperature control zone (maintained at approximately60° C.), where primers bind and are extended through the actions of Taqpolymerase. The cartridge shuttles fluid between these two reactiontemperature zones of the PCR reaction zone and this process is repeatedup to about 45 times resulting in the generation of detectable PCRamplicons. Optionally, additional primers are reconstituted in the thirdchamber and combined with the fluid in the primary flow path, which isthen cycled through the first and second reaction temperature controlledzones once more for amplification of nested sequences. The contents ofthe fourth chamber are reconstituted and directed to the primary flowpath for the final denature step. Preferably, the final denature step isconduct at about 94° C.

In a preferred embodiment, the flow path between the first and secondreaction temperature controlled zones comprises a restriction zone thatenables the use of a pressure sensor to determine the location of theliquid between each reaction temperature controlled zone. When liquidtraverses the restriction zone the driving pressure increases,indicating the position of the liquid in the flow path and allowing forclosed loop control. The restriction zone is depicted in FIG. 3( h). Ina preferred embodiment, the length of the restriction zone is betweenabout 0.1-1.0 inches and more preferably about 0.375 inches, and thecross-sectional width and height are between 5 mils and 40 mils, andmore preferably about 10 mils (1 mil=0.001 inches). Accordingly, theinvention includes a method comprising: i) incubating a fluid slug inthe first temperature controlled zone, ii) using pressure or vacuum tomove the fluid slug through the restriction zone to the second reactionzone, iii) monitoring the applied pressure to determine when the fluidslug has fully passed through the reaction zone and iv) releasing theapplied pressure or vacuum to stop fluid movement and to incubate thefluid slug in the second temperature controlled zone. The invention alsoincludes the analogous method for moving the fluid slug from the secondto the first temperature controlled zone as well as a method for cyclingthe fluid slug between temperatures by repeatedly moving the slugbetween the temperature zones.

The primary flow path leads from the reaction zone outlet to thedetection zone. The detection zone is intersected by a detection reagentmulti-conduit junction connecting (i) the primary flow path and one ormore detection reagent chambers; and (ii) one or more detection reagentchambers and one or more detection reagent air vent ports. The detectionzone is adapted to carry out a physical measurement on the PCR ampliconsproduced in the PCR reaction zone. Detection probes are reconstitutedand directed to the primary flow path, where the probes are mixed withthe PCR amplicons formed in the reaction zone. In a particularlypreferred embodiment, the detection zone is configured to detect PCRamplicons using the nucleic acid detection assay depicted in FIG. 4.Briefly, oligonucleotide probes (41) composed of unique target-specificcapture sequences are immobilized on separate electrodes (42) in thedetection zone. These capture oligonucleotides are thiolated on the 5′end (43) and are covalently coupled to bovine serum albumin (BSA) (44)through sulfoSMCC linker chemistry, and the BSA is adsorbed onto thecarbon-based electrode. Detection probes (45) are composed of uniqueoligonucleotide sequences containing a 3′ biotin residue. These probesare coupled to an ECL-labeled streptavidin (46) at a 1:1 ratio. Both thecapture and detection probes are unique sequences that are internal tothe primer binding sites (47) used for PCR. This approach can be used tominimize possible competitive binding events that can occur in thepresence of free PCR primers. The detection probes and amplicons areincubated in the detection zone, detection buffer is added, thedetection zone is optionally washed, and electrode induced luminescenceis detected.

The detection zone can be configured to conduct an assay in either aone- or two-step format. In a one-step format, the capture surface isexposed to a solution containing both analyte and detection probe in asingle volume and incubated for a specified time before analysis. Atwo-step assay separates the analyte and detection probe: analytesolution is first incubated with the capture surface, followed byaddition of detection probes and a second incubation. A wash step can beincorporated between the two steps to remove any unbound analyte beforethe addition of detection probes. In a preferred embodiment, a one-stepassay format is employed in the detection zone.

Preferably, the electrodes in the assay cartridge are patterned in a twodimensional array along the fluid path. The array and/or fluid path arepreferably in a linear arrangement, although other shapes (e.g., arcs,curves, zig-zags, etc. can also be used). In a preferred embodiment, theprimary flow path in the detection zone is configured to maintainuniform flow through-out the detection zone and the flow path comprisesa square or U-shaped arrangement. Most preferably, the length of theflow path along the direction of flow is greater than the widthperpendicular to the direction of flow, the active area of the electrodetakes up a significant portion of the width of the flow path (preferablygreater than 60%, more preferably greater than 80%), and/or the heightof the flow path above the electrodes is small compared to the width ofthe flow path. In an especially preferred embodiment, the electrodes areimaged using a CCD camera, electrochemiluminescence is triggeredsimultaneously across the entire electrode surface in the detectionzone, and the camera images the entire electrode to detect emittedelectrochemiluminescence.

As illustrated in FIG. 1( c) of copending U.S. Ser. No. 10,744,726,filed Dec. 23, 2003 and the accompanying text, an electrode array(preferably comprised of carbon ink) is applied to the substrate layerto form the electrode, electrical lead, and electrical contact portions.A dielectric layer is preferably applied over the electrode layer todefine assay domains and impedance sensors. Alternatively, electricalcontact can be printed on the opposing side of the substrate andconnected to the electrodes or electrical leads via conductivethrough-holes through the substrate.

Co-pending U.S. patent application Ser. Nos. 10/185,274, filed Jun. 28,2002, 10/744,726, filed Dec. 23, 2003, and 12/959,952, filed Dec. 3,2010, hereby incorporated by reference, provide a number of examples ofelectrode and dielectric materials, electrode patterns and patterningtechniques and immobilization techniques that are adapted for use inelectrode-induced luminescence assays and suitable for use with theassay cartridges of the invention. Electrodes in the present inventionare preferably comprised of a conductive material. The electrode cancomprise a metal such as gold, silver, platinum, nickel, steel, iridium,copper, aluminum, a conductive alloy, or the like. They can alsocomprise oxide coated metals (e.g. aluminum oxide coated aluminum).Electrodes can comprise non-metallic conductors such as conductive formsof molecular carbon. Electrodes can also be comprised of semiconductingmaterials (e.g. silicon, germanium) or semi-conducting films such asindium tin oxide (ITO), antimony tin oxide (ATO) and the like.Electrodes can also be comprised of mixtures of materials containingconductive composites, inks, pastes, polymer blends, metal/non-metalcomposites and the like. Such mixtures can include conductive orsemi-conductive materials mixed with non-conductive materials.Preferably, electrode materials are substantially free of silicone-basedmaterials.

Electrodes (in particular working electrodes) used in assay cartridgesof the invention are advantageously able to induce luminescence fromluminescent species. Preferable materials for working electrodes arematerials able to induce electrochemiluminescence fromruthenium-tris-bipyridine in the presence of tertiary alkyl amines (suchas tripropylamine). Examples of such preferred materials includeplatinum, gold, ITO, carbon, carbon-polymer composites, and conductivepolymers.

Preferably, electrodes are comprised of carbon-based materials such ascarbon, carbon black, graphitic carbon, carbon nanotubes, carbonfibrils, graphite, carbon fibers and mixtures thereof. Advantageously,they are comprised of conductive carbon-polymer composites, conductiveparticles dispersed in a matrix (e.g. carbon inks, carbon pastes, metalinks), and/or conductive polymers. One preferred embodiment of theinvention is an assay cartridge, preferably an assay cartridge, havingelectrodes (e.g., working and/or counter electrodes) that comprisecarbon, preferably carbon layers, more preferably screen-printed layersof carbon inks. Some useful carbon inks include materials produced byAcheson Colloids Co. (e.g., Acheson 440B, 423ss, PF407A, PF407C,PM-003A, 30D071, 435A, Electrodag 505SS, and Aquadag™), E.I. Du Pont deNemours and Co. (e.g., Dupont 7105, 7101, 7102, 7103, 7144, 7082, 7861D,E100735 62B and CB050), Advanced Conductive Materials (e.g., PTF 20),Gwen Electronics Materials (e.g., C2000802D2) and Conductive CompoundsInc (e.g., C-100), and Ercon Inc. (e.g., G-451, G-449 and 150401).

Electrodes can be formed into patterns by a molding process (i.e.,during fabrication of the electrodes), by patterned deposition, bypatterned printing, by selective etching, through a cutting process suchas die cutting or laser drilling, and/or by techniques known in the artof electronics microfabrication. Electrodes can be self-supporting orcan be supported on another material, e.g. on films, plastic sheets,adhesive films, paper, backings, meshes, felts, fibrous materials, gels,solids (e.g. metals, ceramics, glasses), elastomers, liquids, tapes,adhesives, other electrodes, dielectric materials and the like. Thesupport, or substrate, can be rigid or flexible, flat or deformed,transparent, translucent, opaque or reflective. Preferably, the supportcomprises a flat sheet of plastic such as acetate or polystyrene.Electrode materials can be applied to a support by a variety of coatingand deposition processes known in the art such as painting,spray-coating, screen-printing, ink-jet printing, laser printing,spin-coating, evaporative coating, chemical vapor deposition, etc.Supported electrodes can be patterned using photolithographic techniques(e.g., established techniques in the microfabrication of electronics),by selective etching, and/or by selective deposition (e.g., byevaporative or CVD processes carried out through a mask). In a preferredembodiment, electrodes are comprised of extruded films of conductingcarbon/polymer composites. In another preferred embodiment, electrodesare comprised of a screen printed conducting ink deposited on asubstrate. Electrodes can be supported by another conducting material.In some applications, screen printed carbon ink electrodes are printedover a conducting metal ink (e.g., silver ink) layer so as to improvethe conductivity of the electrodes. Preferably, in assay cartridges, aminiaturized design allows the use of electrodes having short printedelectrode leads (preferably less than 1.5 cm, more preferably less than1.0 cm) that are relatively similar in length. By keeping the leadsshort, it is possible to use screen printed carbon electrodes without anunderlying conductive metal layer such as a silver layer.

According to one preferred embodiment of the invention, the electrodesurface (preferably a working electrode surface of an assay cartridge orassay plate) is bounded by a dielectric surface, the dielectric surfacebeing raised or lowered (preferably raised) and/or of differenthydrophobicity (preferably, more hydrophobic) than the electrodesurface. Preferably, the dielectric boundary is higher, relative to theelectrode surface, by 0.5-100 micrometers, or more preferably by 2-30micrometers, or most preferably by 8-12 micrometers. Even morepreferably, the dielectric boundary has a sharply defined edge (i.e.,providing a steep boundary wall and/or a sharp angle at the interfacebetween the electrode and the dielectric boundary).

Preferably, the first electrode surface has an advancing contact anglefor water 10 degrees less than the dielectric surface, preferably 15degrees less, more preferably 20 degrees less, more preferably 30degrees less, even more preferably 40 degrees less, and most preferred50 degrees less. One advantage of having a dielectric surface that israised and/or more hydrophobic than the electrode surface is in thereagent deposition process where the dielectric boundary can be used toconfine a reagent within the boundary of the electrode surface. Inparticular, having a sharply defined edge with a steep boundary walland/or a sharp angle at the interface between the electrode anddielectric boundary is especially useful for “pinning” drops of solutionand confining them to the electrode surface. In an especially preferredembodiment of the invention, the dielectric boundary is formed byprinting a patterned dielectric ink on and/or around the electrode, thepattern designed so as to expose one or more assay domains on theelectrode.

Electrodes can be modified by chemical or mechanical treatment toimprove the immobilization of reagents. The surface can be treated tointroduce functional groups for immobilization of reagents or to enhanceits adsorptive properties. Surface treatment can also be used toinfluence properties of the electrode surface, e.g., the spreading ofwater on the surface or the kinetics of electrochemical processes at thesurface of the electrode. Techniques that can be used include exposureto electromagnetic radiation, ionizing radiation, plasmas or chemicalreagents such as oxidizing agents, electrophiles, nucleophiles, reducingagents, strong acids, strong bases and/or combinations thereof.Treatments that etch one or more components of the electrodes can beparticularly beneficial by increasing the roughness and therefore thesurface area of the electrodes. In the case of composite electrodeshaving conductive particles or fibers (e.g., carbon particles orfibrils) in a polymeric matrix or binder, selective etching of thepolymer can be used to expose the conductive particles or fibers.

One particularly useful embodiment is the modification of the electrode,and more broadly a material incorporated into the present invention bytreatment with a plasma, specifically a low temperature plasma, alsotermed glow-discharge. The treatment is carried out in order to alterthe surface characteristics of the electrode, which come in contact withthe plasma during treatment. Plasma treatment can change, for example,the physical properties, chemical composition, or surface-chemicalproperties of the electrode. These changes can, for example, aid in theimmobilization of reagents, reduce contaminants, improve adhesion toother materials, alter the wettability of the surface, facilitatedeposition of materials, create patterns, and/or improve uniformity.Examples of useful plasmas include oxygen, nitrogen, argon, ammonia,hydrogen, fluorocarbons, water and combinations thereof. Oxygen plasmasare especially preferred for exposing carbon particles in carbon-polymercomposite materials. Oxygen plasmas can also be used to introducecarboxylic acids or other oxidized carbon functionality into carbon ororganic materials (these can be activated, e.g., as active esters oracyl chlorides) so as to allow for the coupling of reagents. Similarly,ammonia-containing plasmas can be used to introduce amino groups for usein coupling to assay reagents.

Treatment of electrode surfaces can be advantageous so as to improve orfacilitate immobilization, change the wetting properties of theelectrode, increase surface area, increase the binding capacity for theimmobilization of reagents (e.g., lipid, protein or lipid/proteinlayers) or the binding of analytes, and/or alter the kinetics ofelectrochemical reactions at the electrode. In some applications,however, it can be preferable to use untreated electrodes. For example,we have found that it is advantageous to etch carbon ink electrodesprior to immobilization when the application calls for a large dynamicrange and therefore a high binding capacity per area of electrode. Wehave discovered that oxidative etching (e.g., by oxygen plasma) hasadditional advantages in that the potential for oxidation of tripropylamine (TPA) and the contact angle for water are both reduced relative tothe unetched ink. The low contact angle for water allows reagents to beadsorbed on the electrode by application of the reagents in a smallvolume of aqueous buffer and allowing the small volume to spread evenlyover the electrode surface. Surprisingly, we have found that excellentassays can also be carried out on unetched carbon ink electrodes despitethe presence of polymeric binders in the ink. In fact, in someapplications requiring high sensitivity or low non-specific binding itis preferred to use unetched carbon ink electrodes so as to minimize thesurface area of exposed carbon and therefore minimize background signalsand loss of reagents from non-specific binding of reagents to theexposed carbon. Depending on the ink used and the process used to applythe ink, the electrode surface may not be easily wettable by aqueoussolutions. We have found that we can compensate for the low wettabilityof the electrodes during the adsorption of reagents by adding lowconcentrations of non-ionic detergents to the reagent solutions so as tofacilitate the spreading of the solutions over the electrode surface.Even spreading is especially important during the localizedimmobilization of a reagent from a small volume of solution. Forexample, we have found that the addition of 0.005-0.04% Triton X-100®allows for the spreading of protein solutions over unetched carbon inksurfaces without affecting the adsorption of the protein to theelectrode and without disrupting the ability of a dielectric filmapplied on or adjacent to the electrode (preferably, a printeddielectric film with a thickness of 0.5-100 micrometers, or morepreferably 2-30 micrometers, or most preferably 8-12 micrometers andhaving a sharply defined edge) to confine fluids to the electrodesurface. Preferably, when non-ionic detergents such as Triton X-100 areused to facilitate spreading of reagents (e.g., capture reagents) ontounetched screen-printed electrodes (i.e., so as to allow theimmobilization of the reagents), the solutions containing the reagentsare allowed to dry onto the electrode surface. It has been found thatthis drying step greatly improves the efficiency and reproducibility ofthe immobilization process.

Electrodes can be derivatized with chemical functional groups that canbe used to attach other materials to them. Materials can be attachedcovalently to these functional groups, or they can be adsorbednon-covalently to derivatized or underivatized electrodes. Electrodescan be prepared with chemical functional groups attached covalently totheir surface. These chemical functional groups include but are notlimited to COOH, OH, NH₂, activated carboxyls (e.g., N-hydroxysuccinimide (NHS)-esters), poly-(ethylene glycols), thiols, alkyl((CH₂)_(n)) groups, and/or combinations thereof). Certain chemicalfunctional groups (e.g., COOH, OH, NH₂, SH, activated carboxyls) can beused to couple reagents to electrodes. For further reference to usefulimmobilization and bioconjugation techniques see G. Hermanson, A. Malliaand P. Smith, Immobilized Affinity Ligand Techniques (Academic Press,San Diego, 1992) and G. Hermanson, Bioconjugate Techniques (AcademicPress, San Diego, 1996).

In preferred embodiments, NHS-ester groups are used to attach othermolecules or materials bearing a nucleophilic chemical functional group(e.g., an amine). In a preferred embodiment, the nucleophilic chemicalfunctional group is present on and/or in a biomolecule, either naturallyand/or by chemical derivatization. Examples of suitable biomoleculesinclude, but are not limited to, amino acids, proteins and functionalfragments thereof, antibodies, binding fragments of antibodies, enzymes,nucleic acids, and combinations thereof. This is one of many suchpossible techniques and is generally applicable to the examples givenhere and many other analogous materials and/or biomolecules. In apreferred embodiment, reagents that can be used for ECL can be attachedto the electrode via NHS-ester groups.

It can be desirable to control the extent of non-specific binding ofmaterials to electrodes. Simply by way of non-limiting examples, it canbe desirable to reduce or prevent the non-specific adsorption ofproteins, antibodies, fragments of antibodies, cells, subcellularparticles, viruses, serum and/or one or more of its components, ECLlabels (e.g., Ru^(II)(bpy)₃ and Ru^(III)(bpy)₃ derivatives), oxalates,trialkylamines, antigens, analytes, and/or combinations thereof). Inanother example, it can be desirable to enhance the binding ofbiomolecules.

One or more chemical moieties that reduce or prevent non-specificbinding (also known as blocking groups) can be present in, on, or inproximity to an electrode. Such moieties, e.g., PEG moieties and/orcharged residues (e.g., phosphates, ammonium ions), can be attached toor coated on the electrode. Examples of useful blocking reagents includeproteins (e.g., serum albumins and immunoglobins), nucleic acids,polyethylene oxides, polypropylene oxides, block copolymers ofpolyethylene oxide and polypropylene oxide, polyethylene imines anddetergents or surfactants (e.g., classes of non-ionicdetergents/surfactants known by the trade names of Brij, Triton, Tween,Thesit, Lubrol, Genapol, Pluronic (e.g., F108), Tetronic, Tergitol, andSpan).

Materials used in electrodes can be treated with surfactants to reducenon-specific binding. For example, electrodes can be treated withsurfactants and/or detergents that are well known to one of ordinaryskill in the art (for example, the Tween, Triton, Pluronics (e.g.,F108), Span, and Brij series of detergents). Solutions of PEGs and/ormolecules which behave in similar fashion to PEG (e.g., oligo- orpolysaccharides, other hydrophilic oligomers or polymers) (“Polyethyleneglycol chemistry: Biotechnical and Biomedical Applications”, Harris, J.M. Editor, 1992, Plenum Press) can be used instead of and/or inconjunction with surfactants and/or detergents. Undesirable non-specificadsorption of certain entities such as those listed above can be blockedby competitive non-specific adsorption of a blocking agent, e.g., by aprotein such as bovine serum albumin (BSA), casein or immunoglobulin G(IgG). One can adsorb or covalently attach an assay reagent on anelectrode and subsequently treat the electrode with a blocking agent soas to block remaining unoccupied sites on the surface.

Electrodes used in the assay cartridges are, preferably, non-porous,however, in some applications it is advantageous to use porouselectrodes (e.g., mats of carbon fibers or fibrils, sintered metals, andmetals films deposited on filtration membranes, papers or other poroussubstrates. These applications include those that employ filtration ofsolutions through the electrode so as to: i) increase mass transport tothe electrode surface (e.g., to increase the kinetics of binding ofmolecules in solution to molecules on the electrode surface); ii)capture particles on the electrode surface; and/or iii) remove liquidfrom the well.

Preferred assay cartridges can use dielectric inks, films or otherelectrically insulating materials (hereinafter referred to asdielectrics). Dielectrics in the present invention can be used toprevent electrical connectivity between electrodes, to define patternedregions, to adhere materials together (i.e., as adhesives), to supportmaterials, to define assay domains, as masks, as indicia and/or tocontain assay reagents and other fluids. Dielectrics are non-conductingand advantageously non-porous (i.e., do not permit transmission ofmaterials) and resistant to dissolving or degrading in the presence ofmedia encountered in an electrode induced luminescence measurement. Thedielectrics in the present invention can be liquids, gels, solids ormaterials dispersed in a matrix. They can be deposited in uncured formand cured to become solid. They can be inks, solid films, tapes orsheets. Materials used for dielectrics include polymers, photoresists,plastics, adhesives, gels, glasses, non-conducting inks, non-conductingpastes, ceramics, papers, elastomers, silicones, thermoplastics.Preferably, dielectric materials of the invention are substantially freeof silicones. Examples of non-conducting inks include UV curabledielectrics such as materials produced by Acheson Colloids Co. (e.g.,Acheson 451SS, 452SS, PF-455, PD039A, PF-021, ML25251, ML25240, ML25265,and Electrodag 38DJB16 clear), Nazdar (e.g., Nazdar GS2081 3400SPL) andE.I. du Pont de Nemours and Co. (e.g., Dupont: 5018, 3571, and 5017).

Dielectrics, in accordance with certain preferred embodiments, can beapplied by a variety of means, for example, printing, spraying,laminating, or can be affixed with adhesives, glues, solvents or by useof mechanical fasteners. Patterns and/or holes in dielectric layers canbe formed by molding processes (i.e., during fabrication of the layer),by selective etching and/or by a cutting process such as die cutting orlaser drilling. Dielectrics can be deposited and/or etched in patternsthrough the use of established photolithographic techniques (e.g.,techniques used in the semiconductor electronics industry) and/or bypatterned deposition using an evaporative or CVD process (e.g., bydeposition through a mask). In a preferred embodiment, a dielectric inkis deposited on a substrate by printing (e.g., ink jet printing, laserprinting or, more preferably, screen printing) and, optionally, UVcured. Preferably, the screen printed dielectric is UV curable allowingfor improved edge definition than solvent based dielectrics. In anotherpreferred embodiment, a non-conducting polymeric film is affixed to asupport using an adhesive.

When using a dielectric ink printed on, or adjacent to, an electrode toconfine fluids to regions of the electrode surface, the dielectric filmpreferably has a thickness of 0.5-100 micrometers, or more preferably2-30 micrometers, or most preferably 8-12 micrometers and also,preferably, has a sharply defined edge with steep walls.

The use of patterned electrodes in cartridges can impose certain uniquedesign and/or performance constraints. In particular, the use ofpatterned electrode leads can lead to problems associated with voltagedrops along the leads, especially in applications likeelectrochemiluminescence that often require relatively high currents.The problems are often greatest when using electrodes comprising thinlayers of only moderately conductive materials such as carbon inks. Theproblem can be partially mitigated by use of multi-layer patternedelectrodes (where the conductivity of an exposed moderately conductivematerial such as a carbon ink is increased by printing it over a moreconductive material such as a silver ink) although this approachintroduces additional manufacturing steps. Alternatively, the problemcan be partially mitigated in systems having multiple assay electrodesby keeping the leads short (preferably, so that the resistance betweenthe electrode and the electrical contact is less than 500 ohms, morepreferably less than 300 ohms, most preferably less than 100 ohms) tominimize the voltage drop and by keeping the leads about the same lengthto make the voltage drop consistent from electrode to electrode.

In an assay cartridge comprising multiple working electrodes, thevariability from electrode to electrode in the voltage drop across theelectrode leads is preferably smaller than the potential applied duringthe course of an assay measurement so that this variability has minimaleffect on the variability of the measurements. In especially preferredembodiments, the variability in voltage drop across the leads is lessthan 20% of the potential applied during the course of an assaymeasurement, more preferably less than 10% or most preferably less than2%. Alternatively, the uniformity in leads can be described in terms ofthe variation in resistance across the leads which is preferably lessthan 50 ohms, more preferably less than 10 ohms, most preferably lessthan 1 ohm.

Where the arrangement of the electrodes and/or contacts makes itdifficult to keep the leads a uniform length, the matching of leadresistances can be accomplished by geometrically matching thelength-to-width ratio of each electrode lead (assuming consistent printthickness). This length-to-width ratio is referred to hereinafter as the“number of squares.” Typically, for a preferred cartridge-basedconfiguration using screen printed carbon inks, the electrode leads areon the order of 4 to 5 squares. Commercially available inks typicallyhave ink resistances that are specified in resistance per square perthickness (e.g., ohms/square/mil) and can vary widely depending on theink selected. In a particularly preferred embodiment, a carbon ink isused that possesses an ink resistance that measures approximately 15ohms/square/mil. The total resistance measured from end-to-end across alead for one preferred embodiment is typically on the order of 450 ohmsfor a configuration utilizing a 5 squares lead.

According to another aspect of the present invention, the electrodesurfaces are coated with assay reagents such as BSA or other specificbinding reagents by dispensing solutions comprising the reagents to oneor more appropriate locations on the electrode array, i.e., the capturesurfaces. Preferably, the assay reagents collect on the surface (e.g.,via the formation of covalent bonds, non-specific adsorption or specificbinding interactions) to form an immobilized layer on the electrode. Ina preferred embodiment, accurate volume delivery to a specified locationresults in complete coverage of only the desired electrode surfaceand/or a desired portion thereof. Accurate volume delivery to aspecified location can be readily accomplished with commerciallyavailable dispensing equipment; e.g., commercially available equipmentfrom BioDot.

Attaining complete coverage of a pre-defined region on a surface (e.g.,an assay electrode) via localized deposition of a liquid (e.g., an assayreagent or a liquid comprising an assay reagent) can be difficult toachieve if the advancing contact angle of the liquid on the surface ishigh, thereby inhibiting spreading of the liquid on the surface (as hasbeen observed for surfactant-free aqueous solutions on untreated carbonink electrodes). Spreading can be accelerated by chemically modifyingthe surface to make it more wettable or by adding surfactants to theliquid, however, in many circumstances it is undesirable to change thephysical properties of the surface or liquid. Alternatively, we havefound that excellent and well controlled spreading of liquids can beachieved on surfaces, such as carbon ink electrodes, having high contactangle hysteresis (i.e., large differences in the advancing andretreating contact angle of the liquid on the surface, preferablydifferences greater than 10 degrees, more preferably greater than 30degrees, more preferably greater than 50 degrees, most preferablygreater than 70 degrees) by using impact-driven fluid spreading. Suchresults can be achieved without surface modification or the use ofsurfactants. Fluid is deposited (preferably, using a fluidmicro-dispenser such as a micro-pipette, micro-syringe, solenoid valvecontrolled micro-dispenser, piezo-driven dispenser, ink-jet printer,bubble jet printer, etc.) on the surface at high velocity (preferablygreater than 200 cm/s, more preferably greater than 500 cm/s, mostpreferably greater than 800 cm/s) so as to drive spreading of the liquidover the surface, despite the high advancing contact angle, to a sizedictated by the volume and velocity of the dispensed fluid. The lowretreating contact angle prevents significant retraction of the fluidonce it has spread. Using the impact-driven spreading technique, it ispossible to coat, with a predetermined volume of liquid, regions of asurface that are considerably larger (preferably, by at least a factorof 1.2, more preferably by at least a factor of two, even morepreferably by at least a factor of 5) than the steady state spreadingarea of the predetermined volume of liquid on the surface (i.e., thearea over which a drop having that volume spreads when touched to thesurface at a velocity approaching zero).

Preferably, the region to be coated is defined by a physical boundarythat acts as a barrier to confine the deposited fluid to the pre-definedregion (e.g., a surrounding ledge or depression, a boundary formed ofpatterned materials deposited or printed on the surface, and/or aboundary formed via an interface with a surrounding region that variesin a physical property such as wettability). More preferably, the liquidhas a higher receding contact angle on the surrounding region than onthe pre-defined region (preferably, the difference is greater than 10degree, more preferably greater than 30 degrees, most preferably greaterthan 50 degrees). Even more preferably, the surrounding region alsoexhibits a low contact angle hysteresis for the liquid (preferably, lessthan 20 degrees, most preferably, less than 10 degrees). By using asurrounding region having high receding contact angle and/or lowhysteresis, the tolerance for imprecision in deposition velocity orspreading rate becomes much improved. In a preferred deposition method,a small volume of reagent is dispensed onto the pre-defined region withsufficient velocity to spread across the pre-defined region and slightlyonto the surrounding region, the liquid then retracts off thesurrounding region (due to its high receding contact angle) but does notretract smaller than the size of the pre-defined area (due to its lowreceding contact angle). In especially preferred embodiments of theinvention the pre-defined area is an exposed area of an electrode(preferably, a carbon ink electrode) and the surrounding region isprovided by a dielectric ink patterned on the electrode.

As described above, assay reagents such as nucleic acids, proteins, orother specific binding reagents can be patterned by depositing (e.g.,via impact driven spreading) solutions comprising the reagents onpre-defined locations on a surface (e.g., an electrode surface,preferably a carbon ink electrode surface) and allowing the reagents tobecome immobilized on the surface (e.g., via covalent bonds,non-specific interactions and/or specific binding interactions).Preferably, the region to be coated is defined by a physical boundarythat acts as a barrier to confine the deposited fluid to the pre-definedregion (e.g., a surrounding ledge or depression, a boundary formed ofpatterned materials deposited or printed on the surface, and/or aboundary formed via an interface with a surrounding region that variesin a physical property such as wettability) so as to form a fluidcontainment region.

In certain preferred embodiments, nucleic acids, proteins or otherbinding reagents (preferably proteinaceous binding reagents) areimmobilized on carbon ink electrodes by non-specific adsorption. It maybe advantageous to allow the assay reagent solution to dry on theelectrode during the immobilization procedure. Preferably, theimmobilization procedure further comprises blocking un-coated sites onthe surface with a blocking agent such as a protein solution (e.g.,solutions of BSA or casein), washing the surface with a wash solution(preferably a buffered solution comprising surfactants, blocking agents,and/or protein stabilizers such as sugars) and/or drying the surface.

In a preferred immobilization procedure of the invention, imprecisiondue to variations in the ability of different assay reagents to adsorbon a surface such as a carbon ink electrode are reduced by immobilizingvia a specific binding interaction involving a first and second bindingpartner. Such an immobilization technique is less likely to be affectedby small variations in the properties of the surface. By way of example,nucleic acids can be patterned by patterned deposition of nucleic acidsolutions (the first binding partner) on a surface coated with a nucleicacid complement (the second binding partner). Alternatively, assayreagents labeled with the first binding partner (preferably, biotin) canbe patterned by patterned deposition of the assay reagents on a surfacecoated with the second binding partner (preferably, anti-biotin,streptavidin, or, more preferably, avidin). Most preferably, the secondbinding partner is deposited in the same pattern as the assay reagents.By analogy, the method can be adapted to use any of a variety of knownfirst binding partner—second binding partner pairs including, but notlimited to, hapten-antibody, nucleic acid—complementary nucleic acid,receptor-ligand, metal-metal ligand, sugar-lectin, boronic acid—diol,etc.

The skilled practitioner will be able to readily select materialssuitable for the fabrication of the cartridges of the invention.Suitable materials include glass, ceramics, metals and/or plastics suchas acrylic polymers (such as Lucite), acetal resins (such as Delrin),polyvinylidene fluoride (PVDF), polyethylene terephthalate (PET),polytetrafluoroethylene (e.g., Teflon), polystyrene, polypropylene, ABS,PEEK and the like. Preferably, the materials are inert to anysolutions/reagents that will contact them during use or storage of thecartridge. In certain preferred embodiments, at least some portion ofthe cartridge is fabricated from transparent and/or translucentmaterials such as glass or acrylic polymer to provide windows that allowoptical interrogation of fluids or surfaces inside the cartridge, e.g.,for analysis of compositions within detection chambers of the cartridgeor for monitoring and controlling the movement of liquids through thefluidic networks defined within the cartridge.

The assay cartridge is preferably adapted and configured to beselectively controlled via a reader instrument. In this regard,reference is made to FIGS. 1(a), 23, and 34, and the accompanying textof U.S. Ser. No. 10/744,726, filed Dec. 23, 2002, and FIGS. 42-46 andthe accompanying text of U.S. Ser. No. 12/959,952, filed Dec. 3, 2010,the disclosures of which are incorporated herein by reference. FIG. 5(a) depicts a simplified schematic of the reader. The reader (50)preferably includes a housing (51), an optical detector (52), and thereader is adapted and configured to receive and position a cartridge(53) and/or the optical detector for processing of the cartridge. Thereader also contains support subsystems that can include one or more ofthe following: sample acquisition/preprocessing/storage subsystem forsample handling; electrical subsystem for electrically contacting thecartridge's electrical contacts and supplying electrical energy toelectrodes within the cartridge detection zone (54); and a controlsubsystem for controlling and coordinating operation of the system andsubsystems and for acquiring, processing and storing the opticaldetection signal.

In a preferred embodiment of the invention, an assay cartridge hasminimal or no active mechanical or electronic components. When carryingout an assay, such an assay cartridge can be introduced into a readerwhich provides these functions. For example, a reader can haveelectronic circuitry for applying electrical energy to the assayelectrodes and for measuring the resulting potentials or currents atassay electrodes. The reader can have one or more light detectors formeasuring luminescence generated at assay electrodes. Light detectorsthat can be used include, but are not limited to photomultiplier tubes,avalanche photodiodes, photodiodes, photodiode arrays, CCD chips, CMOSchips, film. The light detector can be comprised within an opticaldetection system that also comprise lenses, filters, shutters,apertures, fiber optics, light guides, etc. The reader can also havepumps, valves, heaters, sensors, etc. for providing fluids to thecartridge, verifying the presence of fluids and/or maintaining thefluids at an appropriate controlled temperature. The reader can be usedto store and provide assay reagents, either onboard the reader itself orfrom separate assay reagent bottles or an assay reagent storage device.In a preferred embodiment, all assay reagents required for an analysisof a sample are stored within the assay cartridge. The reader can alsohave cartridge handling systems such as motion controllers for movingthe cartridge in and out of the reader. The reader can have amicroprocessor for controlling the mechanical and/or electronicsubsystems, analyzing the acquired data and/or providing a graphicaluser interface (GUI). The reader can also comprise electrical,mechanical and/or optical connectors for connecting to the cartridge.

An exemplary reader is depicted in FIG. 5( b). The reader includes ahousing and an enclosure positioned within the housing (not shown); acartridge tray (51) for holding the assay cartridge (52) during analysisin the reader; and a mounting frame (not shown) in the enclosureconfigured to align the cartridge with one or more reader componentsincluding, but not limited to (i) an optical detection assembly (53)comprising at least one optical detector (54); (ii) an ampoule breakingmechanism (55); (iii) an electrode contact pin assembly positioned overthe cartridge tray (not shown); (iv) a fluidic control manifoldconfigured to drive fluid motion within the fluidic network of thecartridge (56); (v) one or more heater assemblies (57); and (vi) one ormore optical fluid sensors (58).

The ampoules in the cartridge can be broken serially (one at a time) orin parallel (simultaneously or substantially simultaneously). In apreferred embodiment, each ampoule in the cartridge is brokenindependently. A variety of different approaches are available fordriving a hammer element to break an ampoule including but not limitedto directly coupling the hammer to a motor, solenoid or other activedrive element for striking the ampoule with the hammer or,alternatively, by releasing a hammer held under a spring force (in whichcase an active drive element can be used to load a spring). In apreferred embodiment, the cartridge reader comprises a solenoid drivenmechanism configured to break each ampoule in the cartridgeindependently.

The ability to control the temperature of distinct regions of thecartridge with a high degree of precision is particularly preferred. Asdescribed above, an assay cartridge can include a plurality of distincttemperature controlled zones and the accompanying reader includes acartridge tray with thermally isolated aluminum heating and/or coolingblocks, as appropriate, for each temperature controlled zone. As shownin FIG. 6( a-b), heating elements interface with the cartridge through aheater block positioned on the top side and two bottom heater plates.There are at least three distinct heating zones that are formed in theheating block shown in FIGS. 6( a-b). One heating zone (63) isconfigured to heat the purification zone. This purification heater blockis configured to surround the purification zone, allowing for themaximum heat transfer during the drying and elution steps of thepurification process. The other heating zones (61 and 62) are configuredto heat the PCR reaction zone of the cartridge. These zones (61 and 62)maintain two different temperatures for denaturing cycles andanneal/extend cycles. The lower heaters are two flat heaters separatedby an air gap that thermally insulates them from each other. In apreferred embodiment, the heating block is configured to heat the topand bottom surfaces of the cartridge and the primary flow path in thepurification and detection zones is configured to maximize heat transferfor rapid thermal cycling. FIG. 6( c) shows another embodiment of thecartridge and the various temperature controlled zones within. Thecartridge includes a purification zone (64) maintained at about 70° C.,the PCR reaction zone including two temperature controlled regions,i.e., the denature region (65) maintained at about 96° C. and theanneal/extend region (66) maintained at about 60° C., and the detectionzone (67) which is maintained about 20-40° C., preferably 20-35° C., andmost preferably 25-35° C. In a preferred embodiment, the reader furthercomprises a heater/cooling device, e.g., a theromoelectric Peltierdevice, to interface with the detection zone that is capable of bothheating and cooling.

In a preferred embodiment, the step of PCR amplification in thecartridge is allotted approximately 15 minutes or less of the totalcartridge processing time. In order to accomplish between about 35-45cycles of PCR, the time a fluid sample spends between the temperatureset points for denaturing and annealing/extension in each cycle in thedetection zone should be minimized. Two factors that can affect thetotal PCR time are (i) the time elapsed when moving from one temperaturezone to another, and (ii) the time it takes for the fluid sample toreach the temperature set point, which is similar to the ramp rate in aconventional thermal cycler. The time it takes for fluid sample totransition from one temperature zone to another can be adjusted byadjusting the pump speed. In a preferred embodiment, the elapsed timebetween fluid transitions between the two reaction temperaturecontrolled zones in the detection zone is less than 5 seconds, andpreferably less than 1 second. In order to minimize the time for thefluid sample to reach the set point, the detection zone includes aserpentine shape, increasing the fluid surface area contacting theheating surfaces. The channels in the detection zone of the cartridgeare 0.080″×0.020″. This aspect ratio, along with the temperaturefeedback of the heaters and controllers, allows for rapid temperatureincreases and decreases during thermal cycling. Total cycle times ofabout 20 seconds effectively generate PCR signal in as few as 35 cycles.The temperature of each of the temperature controlled zones ispreferably controlled with resistive heating elements and a panel ofWatlow heater controllers with thermocouple feedback control. Thermallyconductive gasket material is preferably used to ensure that there isgood thermal transfer between the heating blocks and the cartridge. Withthis thermal control configuration, the temperature within a temperaturecontrolled zone of the cartridge can be maintained with an accuracy of±0.5° C. In a preferred embodiment, each of the temperature controlledzones can be independently maintained at the appropriate temperature.

The movement of a liquid sample through all of the processing stepsinvolved in the PCR cartridge is controlled by mating vent ports on thecartridge to a fluidic control manifold that seals against thecartridge. The fluidic control manifold includes valves that allow eachvent port to be sealed, opened to ambient pressure or connected to apressure/vacuum source. Accurate fluid movement through the cartridgeusing pressure is achieved through the use of optical sensors to provideclosed loop control. The manifold shown in FIG. 7 is an acrylic piecemade from multiple precision machined acrylic layers that are laminatedtogether using a vapor bonding process. The channels of the manifoldpreferably have a large dimension to reduce resistance and allow a highvolume of air to pass at a relatively low pressure. Preferably, thefluidic control manifold does not come into contact with fluid in thecartridge and is protected by aerosol filters in the cartridge ventports, which reduces the risk of contamination and minimizes the needfor cleaning.

In one embodiment, the fluidic control manifold (70) includes at leasttwo types of valves. The first type is a rotary shear valve (71)composed of two discs with machined apertures/ports, a Teflon stator anda stainless steel rotor. A specific vent on the cartridge (72) is linkedto the pump or to ambient pressure by aligning the corresponding portson the stator and rotor, respectively. Tension between the stator androtor can be adjusted to provide a air tight seal between the discswhile also allowing for free rotation of the discs relative to eachother. Accurate positioning of the rotor is enabled through the use ofan optical encoder. The reader includes at least two rotary shear valvesso that any two vent ports on the cartridge can be addressed at any onetime, i.e., one port is connected to vacuum or pressure, the second isopened to ambient atmosphere and the remaining ports are left sealed. Tostop fluid flow on a fast time scale, two fast-acting solenoid reliefvalves (not shown) are incorporated between the rotary shear valves andthe cartridge that can quickly release the applied pressure with aresponse time of approximately 10 ms. To prevent overheating of thesolenoids, electronic controls of the valves can be included ifnecessary so that they are only powered when needed.

There are at least two types of pumps used in the reader. To generatepressure for liquid movement, a linear actuator driving an air cylinderis used. All liquid movement in the fluidic network is driven from thishigh precision air cylinder. The other pump is a high volume andpressure diaphragm pump. This pump serves only one function during thecartridge processing and that is to dry the integrated purificationmembrane. Drying the extraction membrane serves to drive off anyresidual wash buffer and requires a large volume of air.

Closed-loop feedback control of fluid movement in the cartridge isachieved by monitoring fluid movement in the cartridge through the useof infra-red reflective optical sensors in the reader. These sensors arepositioned beneath the cartridge as shown in FIG. 5( b). The opticalsensors function to feed-back information to control the valves throughclosed-loop deterministic control using a high speed microprocessor. Thedata from the optical sensors is collected in a serial manner toeliminate potential cross-talk and potential false signals that canresult in improper fluid addressing. The response time of the opticalsensor feedback loop is approximately 30 ms, allowing all of the sensorsto be cycled through to generate a complete picture of the location andbehavior of the fluid sample.

The reader is preferably packaged as a single self-contained unit. Inpreferred embodiments employing luminescence based assays, a smallerlight-tight region is incorporated within the overall reader housing.This allows the luminescence based assay to be performed within thelight tight enclosure to ensure that the readings are not affected byambient light. Preferably, electronic components and otherheat-generating components are located outside of the light tightenclosure.

The cartridge handler subsystem preferably includes a motor to draw thecartridge into the cartridge housing and selectively position thecartridge within the reader; e.g., position the cartridge under asensor/detector. In one preferred embodiment, retraction of thecartridge within the reader housing can be mechanically coupled to oneor more mechanisms within the reader for synchronized/coordinatedoperation of the linked mechanisms. For example, the retraction of thecartridge can be mechanically coupled to: the mechanism for closing thedoor to the light tight enclosure after the cartridge has entered thechamber; the assay electronics subsystem (described in greater detailbelow) to allow the reader's electrical contacts to engage thecartridge's electrical contacts, i.e., be placed into electrical contactwith the electrode array's electrode contacts; the fluidic handlersubsystem's fluidic control manifold to engage the cartridge's fluidports, i.e., be placed into fluidic communication with the cartridge'sfluidic ports (e.g., establishing a pressure seal between thecartridge's fluidic ports and the fluid control manifold); and/or thefluid handler subsystem's reagent cartridge breaking mechanism to allowthe reagent cartridges such as ampoule(s) to be broken during thecartridge retraction/positioning step.

In a preferred embodiment a barcode reader is incorporated on/within thereader to preferably automatically scan an identifying mark/label on thecartridge; e.g., as it is drawn into the reader. The label can containencoded information relating to the specific assays that are to beperformed, calibration parameters and/or any other information requiredto perform the assay.

The assay electronics subsystem preferably includes electrical contacts,sensors and electronic circuitry. The electrical contacts are preferablyadapted and configured to be placed into electrical contact with theelectrode array. In one preferred embodiment, the reader's electroniccircuitry can include analog switching and trans-impedance amplificationcircuits to address a specific pair of electrodes (i.e., pair-wisefiring, discussed in greater detail above) and apply a predefinedvoltage waveform to the circuit formed by that electrode pair. Theactual output voltage and current can be optionally measured fordiagnostic purposes. Preferably the electronic circuitry is also capableof applying an AC waveform (e.g., 500 Hz or less) for capacitive orconductive measurements (as discussed above).

In one particularly preferred embodiment of the reader configured toperform luminescence based assays, the reader can employ an opticaldetector, e.g., a photodiode (most preferably, a cooled photodiode),photomultiplier tube, CCD detector, CMOS detector or the like, to detectand/or measure light/luminescence emanating from the read chambers. If acooled photodiode is employed, a thermo-electric cooler and temperaturesensor can be integrated into the photodiode package itself providingfor selective control by the electronic control system.

A computerized control system is preferably utilized to selectivelycontrol operation of the cartridge-based system. The computerizedcontrol system can be fully integrated within the reader, separated fromthe reader in an externally housed system and/or partially integratedwithin and partially separated from, the reader. For example, the readercan be configured with external communications ports (e.g., RS-232,parallel, USB, IEEE 1394, and the like) for connection to a generalpurpose computer system (not shown) that is preferably programmed tocontrol the reader and/or its subsystems. In one preferred embodiment, asingle embedded microprocessor can be used to control the electronicsand to coordinate cartridge operations. Additionally, the microprocessorcan also support an embedded operator interface, connectivity and datamanagement operations. The embedded operator interface can preferablyutilize an integrated display and/or integrated data entry device (e.g.,keypad). The computerized control system can also preferably includenon-volatile memory storage for storing cartridge results and instrumentconfiguration parameters.

Preferably, the reader has a cartridge handling subsystem thatmechanically engages the cartridges and moves/aligns it into position.Preferably, this process includes positioning the cartridge within alight-tight enclosure. The reader also makes the appropriate fluidicand/or electronic connections to the cartridge and, optionally, breaksor pierces any reagent chamber (e.g., reagent ampoules) present incartridge reagent chambers. As discussed above, in one preferredembodiment, the cartridge handler's motion would be physically coupledto the fluidic and electronic handlers (and, optionally, the reagentcartridge release mechanism) such that upon positioning the cartridgewithin the light tight enclosure the electrical contacts and thefluidics manifold engage the cartridge at their respective engagementpoints (and, optionally, the reagent cartridge release mechanismsreleases reagent from any reagent cartridges). Next, where required orpreferred, the electronic control system begins operating one or moreheating elements in order to bring a zone of the cartridge, i.e., thepurification zone (the pre-heating region, the additional temperaturecontrolled region in the purification zone, or both), the first and/orsecond reaction temperature controlled zones in the reaction zone, andthe detection zone, to the appropriate predetermined temperature andmaintain the cartridge at such target temperature.

The assay cartridges can be used for multiplexed detection of one ormore biological agents in a sample, e.g., bacteria, viruses, biologicaltoxins, and the like. A “biological agent” refers to any biologicalmaterial that can be identified, e.g., cells, viruses, naturallyoccurring proteins, glycoproteins, complex and simple sugars, nucleicacids, lipids, and lipoproteins, as well as toxins, particularly nucleicacid and protein-based toxins, both natural and synthetic. Anon-exemplary list of biological agents that can be detected using thecartridge and methods of the invention include pathogens associated withupper respiratory infection (e.g., influenza A, influenza B, RespiratorySyncytial Virus, Streptococci species), pathogens found in food andwater (e.g., salmonella, listeria, cryptosporidia, campylobacter, E.Coli 0157, etc.), sexually transmitted diseases (e.g., HIV, syphilis,herpes, gonorrhea, HPV, etc.), and blood borne pathogens and potentialbioterrorism agents (e.g., pathogens and toxins in the CDC lists ofSelect A, B and C agents such as B. anthracis, Y. pestis, small pox, F.tularensis, ricin, botulinum toxins, staph enterotoxins (including butnot limited to methicillin-resistant Staphylococcus aureus (MRSA)),Vancomycin Resistant Enterococcus (VRE), Clostridium difficile,Enteroviral meningitis, etc.). Preferred panels also include nucleicacid arrays for measuring mRNA levels of mRNA coding for cytokines,growth factors, components of the apoptosis pathway, expression of theP450 enzymes, expression of tumor related genes, pathogens (e.g., thepathogens listed above), etc. Preferred panels also include nucleic acidarrays for genotyping individuals (e.g., SNP analysis), pathogens, tumorcells, etc.

In a particularly preferred embodiment, the cartridge includes at leasta panel of the following eight agents, with two DNA or RNA sequencestargeted per agent: Bacillus anthracis (BA), Yersinia pestis (YP),Francisella tularensis (FT), Brucella species, Variola virus (smallpox),Ebola virus, Marburg virus, and Venezuelan Equine Encephalitis (VEE).

The present invention also includes kits. The kits can includedisassembled components necessary to make an assay cartridge of theinvention. Alternatively, the kits can comprise, in one or morecontainers, an assay cartridge of the invention and at least oneadditional assay reagent necessary to carry out an assay. The one ormore assay reagents can include, but are not limited to, bindingreagents (preferably, labeled binding reagents, more preferably bindingreagents labeled with electrochemiluminescent labels) specific for ananalyte of interest, ECL coreactants, enzymes, enzyme substrates,extraction reagents, assay calibration standards or controls, washsolutions, diluents, buffers, labels (preferably,electrochemiluminescent labels), etc.

The invention includes assay cartridges (preferably assay cartridges)and readers (preferably readers) as described above. These can besupplied as separate components. The invention also includes assayssystems that comprise an assay cartridge (preferably a cartridge) and areader (preferably a reader).

EXAMPLES Example 1 Nucleic Acid Extraction and Purification

Approach Used for Nucleic Acid Extraction and Purification. Nucleicacids are extracted from a sample by lysis in a guanidine isothiocyanate(GuSNC) buffer. Purification of nucleic acid from potential interferentsin clinical samples is achieved by binding nucleic acid to a silicamatrix in the presence of GuSCN. To test this method, multiple types ofpurification matrices were tested in a prototype mini-column componentto determine which would have the highest binding capacity and whichcould be readily incorporated into a small format suitable for thecartridge of the invention. Whatman glass fiber membranes (types GF/Dand GF/F; available from Whatman Ltd.), 3M Empore membranes (availablefrom 3M, St. Paul, Minn., and Sigma size-fractionated silica dioxideparticles (available from Sigma-Aldrich Co., St. Louis, Mo.) were testedas possible candidates. Whatman GF/D, GF/F, and 3M Empore, were testedand compared for total nucleic acid binding capacity. Whatman GF/D wasfound to have the highest binding capacity compared to the othermatrices (about 8.3 ug/mg). Most importantly, GF/D can readily beintegrated into a fluid flow path of a cartridge and the total bindingcapacity of the membrane can be adjusted by simply adding additionallayers of GF/D.

Buffers for nucleic acid extraction and purification were initiallyformulated and optimized using spin column methods. Furthercharacterization and optimization was then carried out using amini-column prototype (FIG. 8) to facilitate incorporation of a membraneinto a cartridge and to examine fluid flow through the membrane underconditions that mimic those expected in a cartridge. The interior of theprototype included a similar geometry to what would be used in acartridge, including a support frit, a pre-compression mechanism, andfeatures designed to minimize unwanted fluid retention. Using thisprototype, the thickness and aspect ratio of the membrane was optimizedto minimize the retention of fluid. It was found that using two layersof GF/D membrane discs, each with a diameter of 0.81″ was preferable.Design approaches were also developed to securely hold the membrane inplace and to provide pre-compression of the membrane to reducefluctuations in the volume of the membrane as it is wet with differentsolvents.

The extraction prototype system consisted of a small column and a pumpto pull air/buffer through the column, along with a pressure sensor andassociated fluidic lines. Pressure, pump speed, and flow volume throughthe purification column were controlled. Using this prototype, a liquidsample, mixed with GuSCN lysis buffer, was passed through thepurification column to bind nucleic acids. Wash buffers (lysis bufferand ethanol) were sequentially passed through the column to removecontaminants. Finally, the purification matrix was dried by air flow andheated before introduction of elution buffer (a low ionic strengthaqueous buffer) to release the bound nucleic acid.

Practical Considerations Relating to Flow of Samples and Buffers throughGlass Fiber Membranes. An important factor considered duringpurification matrix optimization was ensuring that the column geometryfacilitated homogeneous flow across the diameter of the column whendriving fluids with air pressure. Testing of designs with differentaspect ratios (thickness/diameter) revealed that higher aspect ratiocolumns had more homogeneous flow and had lower retention of fluid. Whendrying a low aspect ratio column by passing air through the column,drying of a small region of the membrane surface provided a lowresistance pathway that essentially prevented complete drying across thediameter of the membrane. High aspect ratio columns provided moreefficient capture of nucleic acids, probably because the entire volumeof the column was more evenly interrogated. The goal in the extractionand elution steps was to recover the DNA/RNA in the smallest possiblevolume, which could be used as the starting material in theamplification process. A small extraction volume will facilitate rapidthermocycling and will allow for a compact cartridge design. Theretention volume of the prototype purification chamber geometry andaspect ratio was about 4 uL.

In the cartridge design, fluid movement is driven by application of airpressure or vacuum. Another consideration in the design of thepurification component is ensuring that samples and purificationreagents can be driven through the GF/D membrane at reasonable flowrates (compatible with the 15 minutes allocated for sample lysis andpurification in the assay cartridge) using reasonable pressures (i.e.,less than about 0.5 atm or about 7 psi) that will not compromise sealswithin the cartridge. FIG. 9 presents pressure traces for a typicalpurification of DNA from a model organisms using the mini-columnprototype and shows the pressures created during i) loading of samplesin GuSCN lysis buffer; ii) washing of the column with clean GuSCN lysisbuffer (buffer 1) and ethanol (buffer 2); iii) drying of the column withair flow; and iv) elution of nucleic acid with low ionic strengthelution buffer. Briefly, 100 uL of an overnight E. coli culture waslysed in GuSCN and purified on a GF/D membrane in a mini-column fixture.Fluid movement was driven by vacuum created by an air cylinder (syringe)run at a speed of 1 to 2 mL per minute for fluid movement steps or 273mL/min for air drying.

A number of different clinical matrices of different viscosity weretested with the mini-column prototype. Whole blood samples (viscosity ofabout 4 cps) were readily processed and produced pressure profilessimilar to that presented in FIG. 9, although with a slightly higherpressure during sample loading (about 5 psi). Sputum yielded significantelevation of pressure during sample loading (the viscosity of sputum canbe in the hundreds of cps). This effect could be markedly reduced bytreating sputum samples with a reducing agent dithiothreitol (DTT) todecrease viscosity prior to loading. FIG. 10 demonstrates that, relativeto untreated sputum, up to 50 times more DTT-treated sputum could beloaded while maintaining acceptable pressures. Briefly, test sampleswere homogenized by the addition of an equal volume of phosphatebuffered saline and vortexed with 2 mm glass beads to make 1× stock.Serial dilutions were then made and either treated with 0.1% DTT at roomtemperature for 1 hour (triangles) or untreated (diamonds). Replicateswere then purified in the mini-column prototype while monitoring columnpressure. The data shows the highest observed pressure as a function ofthe sputum dilution (1=undiluted). The highest concentration point foreach sample type is the highest concentration that could be run withoutexceeding the pressure specification.

Efficiency of Nucleic Acid Purification. Using the prototypemini-column, the effect of temperature on nucleic acid elutionefficiency was also investigated. Optimal elution of nucleic acid fromthe purification matrix was done by increasing the temperature of theelution buffer and GF/D matrix to 70° C. This information aided in thedesign of the final cartridge and reader as it led to the incorporationof heating elements to allow the purification matrix to achieve theoptimal temperature for nucleic acid elution. FIG. 11 shows thatmultiple types of nucleic acid, including genomic DNA, plasmid DNA, andtotal bacterial lysate (containing both genomic DNA and RNA) could becaptured and eluted from the purification membrane. Briefly, purifiedhigh molecular weight genomic DNA from calf thymus, purified plasmidDNA, or a bacterial lysate containing a mixture of high molecular weightgenomic DNA and RNA of various sizes were all subjected to purificationusing the nucleic acid extraction and purification prototype. For eachsample type the flow-through (FT) material and the eluted material wereretained for comparison. After purification, the eluate and the pooled(low-through fractions were resolved on a1% agarose gel and visualizedwith ethidium bromide staining. The absence of bands in the lanes forflow-through material (nucleic acid that was not captured during sampleloading) shows that capture of nucleic acid was very efficient. The oneexception was high molecular weight calf thymus genomic DNA; some DNAwas observed in the flow-through, although greater than 50% of the DNAwas captured on the membrane. High levels of purity could be achievedusing the prototype. The column washing protocols routinely achievedwash qualities of 1 to 10 parts per 100,000, a level that was found tobe sufficient to remove potential interferents of Taq polymerase inclinical samples, such as hemoglobin, anti-coagulants (like EDTA), humicor fulvic acids, and residual lysis buffer components.

FIG. 12 provides PCR amplification results for nucleic acids spiked intoclean buffer, whole blood or a solution containing 1 ug/uL humic andfulvic acids. 100 fg of DNA from B. anthracis was spiked into PBS(buffer only, light grey bars), whole blood (Blood spike—dark greybars), or a buffer sample containing 1 ug/uL humic acid and fulvic acid(humic Spike—white Bars). Samples were then either purified using theextraction prototype (+Purification) or not (−Purification). Eluate fromthe purified samples or material from the unpurified samples wasamplified by PCR to determine the effects of purification and removal ofpotential PCR inhibitors. After amplification the samples were analyzedusing 16-plex assay plates. FIG. 12 shows recovery and detection of theBA. Without purification, blood and humic acid completely inhibited thePCR reactions, reducing the assay signals to background levels. Usingthe purification prototype column and protocol we were able to recoverthe PCR assay signals in these matrices and generate signals that wereroughly equivalent to those observed in clean buffer (PBS).

Efficiency of Cell Lysis Protocol. The use of lysis buffer to achieveefficient lysis of a number of gram positive and gram negative modelbacteria was demonstrated in the prototype purification system. In onestudy, vegetative Bacillus anthracis (Ames strain non-encapsulated) wasused to validate the performance of cell lysis and nucleic acidpurification protocols and to compare them to a standard laboratorymethod. The lysis procedure was robust enough to completely lyse thevegetative bacteria in a about 2 minutes. Moreover, this methodoutperformed a conventional, multi-step labor intensive lysis method(Qiagen), when compared in parallel. The CT values for the real-timeanalysis of the eluted product are shown in FIG. 13. Briefly, vegetativenon-encapsulated B. anthracis (Ames strain) were lysed and purifiedusing either the lysis buffers and methodology described hereinabove orthe Qiagen QiaAmp procedure. CT values obtained by the present methodwere lower or comparable to those obtained with the Qiagen method.Colony formation analysis was done using aliquots of the target organismbefore and after addition of lysis buffer. There were no viable bacteriaafter the addition of lysis buffer, confirming the efficacy of the lysisbuffer in lysing bacterial cells.

Example 2 Nucleic Acid Amplification

Primer Selection. To amplify 16 gene targets (8 agents, 16 gene targetsincluding 6 RNA and 10 DNA targets), primers were used that had beenselected for real time PCR assays. The primers generated amplifiedproducts that were long enough to allow for detection of amplifiedproduct through the use of probes directed to the sequences between thepriming regions. In some cases small changes were made to the primers(slight changes in length or small shifts along the target sequence) toimprove amplification efficiency or to ensure that all the primers hadsimilar melting temperatures The final primer sequences are provided inFIG. 14.

Reverse Transcription Assay Formulation. Three of the pathogens in thefinal reaction cocktail had RNA genomes: Venezuelan Equine Encephalitisvirus (VEE), Marburg virus (MV), and Ebola virus (EV) In order toamplify the two targets associated with each of these pathogens, areverse transcription (RT) step was necessary. To reduce the number ofoligonucleotide primers present in the final RT reaction cocktail, allRT reactions utilized the reverse PCR primer as the first strandsynthesis primer. This method of cDNA synthesis should also conveyanother level of specificity as only cDNA templates specific for thetarget of interest will be synthesized.

During preliminary studies of RT conditions, we found that the presenceof reverse transcriptase can have severe inhibitory effects onsubsequent PCR reactions. This effect is known (Sellner L N et al.,Nucleic Acids Res. 1992, 20, 1487-90) and is usually avoided by dilutingthe RT product before performing PCR, a procedure that would complicateprocessing in a cartridge format. Instead of diluting the RT product, wewere able to eliminate the effect of RT on the PCR reaction byminimizing the amount of reverse transcriptase in the RT mixture andadding tRNA to the reaction mixture. To test RT interference on DNAamplification, we took a DNA target (FT) and processed it using the fullRT and PCR protocol. We tested both a one step RT&PCR protocol (allprimers present through RT and PCR steps) and a two step RT&PCR protocol(only reverse PCR primers for RNA targets present during RT step). FIG.15 shows that addition of tRNA completely reverses the inhibitory effectof RT enzyme on PCR (see Panel B). Panel A shows the amplification of aDNA target (FT) using our 16-plex primer mix and a one step RT and PCRprotocol (all primers for DNA and RNA targets present during RT step).Panel B shows the amplification of the same DNA target (FT) using twostep RT and PCR protocol (only the reverse primers for the RNA targetswere present during the RT step—remaining primers were added aftercompletion of RT step. In both cases we compared different RT enzymes:Superscript II (Lanes 1,2), Superscript III (Lanes 3,4), MMLV (Lanes5,6) or No RT enzyme (Lanes 7,8). We also compared running the reactionsin the presence (Lanes 1, 3, 5 and 7) or absence (Lanes 2, 4, 6 and 8)of 0.2 ug/r×n Yeast tRNA. Each reaction was carried out using 1 pg of FTDNA, a 10 min, 46° C. RT step and 33 cycles of PCR (45 s at 94° C. and60 s at 63° C.). The results show that i) the presence of tRNA isimportant to prevent RT from inhibiting amplification of DNA targets;ii) the two-step protocol provides cleaner PCR products than theone-step protocol and iii) there is little difference between the RTenzymes in the two-step protocol, however, SuperScript III showed thelowest levels of amplification artifacts in the one-step protocol.

Incubation time for reverse transcription was also optimized using RNAtargets. To determine this we used a fixed amount of VEE, MV, or EV RNAand ran RT at 46° C. for between 30 seconds and 6 min. After the RTreaction, the RT was inactivated at 97° C. (a condition that alsoactivates Taq polymerase) and the DNA RT product was amplified by 33cycles of PCR. We found that RT times as short as 2 minutes weresufficient to allow for detection of RNA targets (data not shown).

Optimization of PCR Conditions. Initial work on optimizing PCRamplification conditions for our 16-plex amplification reaction wascarried out using a conventional thermocycler to allow for rapidevaluation of many different reaction parameters. To somewhat mimic thethermocycling approach that will be used in the cartridge (movement offluid between two temperature zones) we chose a commercial thermocycler(the Robo-Cycler) that operates by moving reaction tubes between heatblocks held at different temperatures.

To achieve efficient amplification, we investigated severalinter-related reaction parameters: i) the effect of PCR cycle time,balancing between the ability to run more cycles in a 15 minute periodand the lower amplification efficiency of faster PCR cycles; ii) for agiven cycle time, the optimal ratio of time spent in the anneal/extendphase vs. time spent in the denaturation phase; and iii) we optimizedanneal/extend and denaturation temperatures for rapid amplificationconditions. Detection of the amplified products was conducted inmulti-well plates using a multiplexed ECL sandwich hybridization formatas described hereinbelow.

FIG. 15( c) shows the results of an experiment using a model 6-plex PCRassay to examine the tradeoff between PCR cycle duration and the numberof PCR cycles that can be run in a 15 min amplification reaction. DNA(100 fg of BA, FT or YP DNA) was amplified using a 15 minute 6-plexamplification protocol (2 gene targets per organism). The number of PCRcycles in that 5 min. amplification protocol was varied from 30 to 45cycles by adjusting the duration of each cycle from 20 to 30 seconds.Products were analyzed in a six-plex ECL sandwich hybridization assay.The graph shows that optimal signal was observed when 40-45 cycles wererun. In this experiment, 60% of each cycle was dedicated to theanneal/extend step (at 54° C.) and 40% of each cycle was dedicated todenaturation (at 95° C.).

FIG. 16( a) shows that for the BA-PA target, an annealing temperature of56° C. and a cycle dedicating 60% of cycle time to the anneal/extendstep gave optimal amplification when using a fast (20 sec.) overallcycle time. The graph also shows that these values provide goodrobustness to small changes in temperature or anneal/extend time. Inthis experiment, BA DNA was amplified under 45 cycles of PCR using a 20second PCR cycle time and a denaturation temperature of 95° C. Theannealing temperature was varied as was the percentage of time in eachPCR cycle allocated to the anneal/extend step. The graph shows theamount of BA-PA amplification product as measured using an ECL sandwichhybridization assay. Similar results were observed with other targets.FIGS. 16( b)-(e) show that the optimal denaturation temperature for fastPCR cycles was between 95 to 97° C. BA DNA (100 fg) was amplified in a15 minute total PCR assay time using 45 cycles (8 sec denature-12 secanneal/extend). Different combinations of anneal/extend and denaturationtemperatures were tested. The BA-PA and BA-CAP amplification productswere measured by ECL sandwich hybridization assay. We note that we rantests with thermocouples in amplification tubes to confirm that theamplification solutions actually reached the set anneal/extend anddenaturation temperatures during temperature cycling.

Demonstration of Amplification in PCR Reaction Flowcell Prototype. Inthe cartridge of the invention, PCR amplification is achieved by movingthe reaction mixture between two different temperature zones. Wedeveloped injection molded PCR flow cell prototypes to test out theapproach in a simplified system. We also developed an amplification testbed with heating elements to hold the flow cell and establish the twotemperature zones on the cartridge (FIG. 17). After loading a sampleinto the flow cell, an air cylinder pump was used to apply airpressure/vacuum to cycle the sample slug between the two temperaturezones. Bubble formation can be mitigated by incorporating energydirectors on one of the surfaces and using ultrasonic welding to form asmooth interface between the parts. Uniform heating was achieved byproviding heating elements on the top and bottom of the flow cell. Weused thermocouples in the flow cell to verify that solutions in the flowcell could be cycled between the optimal anneal/extend and denaturingtemperatures using our optimal 20 second PCR cycle times, as determinedbased on experiments using the Robocycler thermocycler.

The optimized 16-plex PCR protocol and reagents developed using theRobocycler were transferred to the flow cell format. Experiments todetermine the optimal amplification efficiency across all assays wereused to compare the flow cell prototype and the Robocycler. To determineamplification efficiency, a known amount of synthetic material,previously calibrated to give a desired signal in an ECL hybridizationassay, was used as the target for amplification. A target level thatgenerated a measurable ECL readout after 10 cycles of amplification butdid not saturate either the detection or amplification system wasselected. This method of measuring amplification efficiency reduces thepotential variability introduced when extensive amplification through35-45 cycles is used. In an ideal reaction, each PCR cycle will resultin a doubling, equal to an amplification factor of 2 per cycle. Giventhe need for single copy detection, we wanted to achieve a minimumamplification factor of about 1.7 for all assays in the multiplex. Evenat a lower amplification factor of 1.6, 45 cycles of amplificationshould give a total amplification of >10⁹, which should be more thansufficient for single molecule detection given that the detection limitof our ECL hybridization assays is typically less than 10⁷ copies.

FIG. 18 is a table of amplification efficiencies measured in the flowcell prototype for each of our 16 targets. Most of the assays haveamplification factors well above our selected goal. The table alsoprovides amplification efficiencies measured using the Robocyclerthermocycler; there was no significant difference between amplificationin the flow cell/test-bed and amplification using the commercialthermocycler.

We also tested the ability of the PCR amplification flow cell prototypeand test-bed to efficiently amplify genomic DNA using our optimizedquick cycling PCR amplification protocol (20 second cycle time exceptfor an initial 90 second denaturation step to fully unfold the genomicDNA and to activate the Taq polymerase). Amplified DNA was then removedfrom the flow cell tested in an ECL sandwich hybridization assay asdescribed in detail hereinbelow, FIG. 19( a)-(d) shows results foramplification of SA genomic DNA. We found that we could detect 100 fg ofSA genomic DNA with high signal to background in as few as 35 cycles.For this level of genomic material, there was only minimal improvementin signal by increasing the number of cycles to 45, suggesting that theamplification reaction has already reached saturation at 35 cycles andthat effective amplification could be achieved in as little as 12minutes (35 cycles×20 seconds per cycle=˜12 min.).

Example 3 Nucleic Acid Detection

Construction of Nucleic Acid Detection Assay. Detection of targetamplicons was performed using a sandwich hybridization format usingelectrochemiluminescence technology (FIG. 4). To allow for ahigher-throughput evaluation of critical parameters, the detectionassays were initially developed and optimized in a 96-well plate formatusing Meso Scale Diagnostics, LLC (MSD, Gaithersburg, Md.) commercialMULTI-ARRAY® plate consumables and SECTOR® Imager plate readers. Theseplates have integrated carbon ink electrodes in each well that serve asboth solid phase supports for binding assays as well as the source ofelectrical energy for ECL measurements. As shown in FIG. 4, eachamplified target was measured by binding it to two oligonucleotideprobes: a capture probe that was immobilized on the carbon ink electrodeand a detection probe that was linked to an ECL label. Binding of theprobes was measured by applying an electrical potential to the electrodeand measuring the emission of light from the ECL label. The two probesequences were selected to bind the target between the primer bindingregions, to eliminate potential interference from the primers and toprovide an additional level of specificity for the targets. Probeselection software was used to ensure that the probes had roughly thesame melting temperatures, were specific for the target organism andwould not bind human DNA. The final probe sequences are provided in FIG.20( a).

The capture probe arrays were immobilized on the electrode by directadsorption from arrays of drops of solution printed on the electrodes.To enhance direct adsorption, we use 5′ thiolated capture probes thatare pre-linked to BSA, through SMCC linker chemistry. Previous studieshave demonstrated that this method works well to provide reproducibleimmobilization of the probes while ensuring that they are properlypresented so that they bind their target sequences. BSA with variousamount of attached capture probes were tested, from 1:1 to 10:1challenge ratio, and it was found that challenge ratios greater than 5:1generated the highest ECL signals for the model assays tested.

Arrays of the capture probes were printed in the wells of MULTI-ARRAYplate using custom array printing instruments. The detection probes werelabeled with a 3′ biotin residue. The detection probes were pre-bound,at a 1.1 ratio, to streptavidin labeled with an ECl label (SULFO-TAG™)so that formation of a sandwich hybridization complex could be detectedby ECL. Detection probes are composed of unique oligonucleotidessequences containing a 3′ biotin residue.

Optimization of the Sandwich Hybridization Assay Format. Initial assayoptimization was carried out in our multi-well plate format, allowing usto efficiently optimize a number of factors including probeconcentrations, buffer formulations, probe sequence selection anddevelopment of procedures and reagents for blocking probe arrays toreduce non-specific binding As part of this task we compared runninghybridization assays as one-step or two-step reactions. In a one-stepassay, the amplified product is mixed with the capture and detectionprobes simultaneously. In a two-step assay, the product is first boundto the immobilized capture probe and is then-allowed to bind to thedetection probe (optionally, after first washing away unbound sample).In either format, the array is washed and an ECL Read Buffer (MSD T ReadBuffer, available from Meso Scale Diagnostics, LLC, Gaithersburg, Md.)is added, prior to conducting the ECL measurement. As a last step of ourPCR amplification reactions, we add Taq inhibitors and then run adenaturing reaction to dehybridize the double stranded products and makethem accessible for binding to the capture and detection probes.

We found that amplification products for some targets gave lower thanexpected signals in our hybridization assays. For example the fulllength amplicons generated from VEE 5′UTR and NSP4 provided much lowerECL signals than short synthetic targets containing only the capture anddetector probe binding regions. We speculated that this difference ismost likely due to the formation of internal loops or folds in thetarget amplicons that block binding of the capture or detector probes.We found two approaches that could be used to recover the signal toexpected levels. The first approach involves adding short pieces ofblocking DNA to the hybridization reaction. The blocking DNA sequencesare selected to be complementary to regions in the target sequence thatare involved in formation of secondary structure (so as to blockformation of the secondary structure) but are also selected such thatthey do not overlap with the probe binding sequences. The secondapproach involves redesigning the PCR primers: we shift the position ofone of the primers on the target sequence to shorten the length of theamplicon and remove nucleotides involved in secondary structureformation (FIG. 20( b) and Table 1 below).

TABLE 1 VEE-5′UTR Current Primer/Probe Set: GAGCTTCCCGCAGTTTGAGGTAGAAGCCAAGCAGGTCACTGATAATGA CCATGCTAATGCCA GAGCGTTTTCGCATCTGGCTTCAAAACTGATCGAAACGGAGGTGGACCC (SEQ ID NO: 1) Primer GAGCTTCCCGCAGTTTGAAAACGGAGGTGGACCC (SEQ ID NO: 2) Detector GCCAAGCAGGTCACT (SEQ ID NO: 3)Capture GACCATGCTAATGCCA (SEQ ID NO: 4) Blocking PiecesGAGCTTCCCGCAGTTTGAGGTAGAA GAGCGTT TTCGCATCTGGCTTCAAAACTGATCGAAACGGAGGTGGACCC (SEQ ID NO: 5) VEE-5′UTR New Primer/Probe Set:GAGCTTCCCGCAGTTTGAGGTAGAAGCCAAGCAGGTCACTGATAATGACCATGCTAATGCCAGAGCGTTTTCGCATCTGGCTTCA (SEQ ID NO: 6) PrimerGAGCTTCCCGCAGTTTGA CGTTTTCGCATCTGGCTTCA (SEQ ID NO: 7) DetectorGTAGAAGCCAAGCAGG (SEQ ID NO: 8) Capture GATAATGACCATGCTAATG(SEQ ID NO: 9) Blocking Pieces — VEE-NSP4 Current Primer/Probe Set:CTTGGCAAACCTCTGGCAGCAGAC GATGAACATGATGATGACAGGAG AAGGGCATTGCATGAAGAGTCAACACGCTGGAACCGAGTGGGTAT (SEQ ID NO: 10) Primer CTTGGCAAACCTCTGGCAGCCGCTGGAACCGAGTGGGTAT (SEQ ID NO: 11) Detector GATGAACATGATGATGAC(SEQ ID NO: 12) Capture GGGCATTGCATGAAG (SEQ ID NO: 13) Blocking PiecesCTTGGCAAACCTCTGGCAGCAGAC GTCAACACGCTGGAACCGAGTGGGTAT (SEQ ID NO: 14)VEE-NSP4 New Primer/Probe Set:GGCAGCAGACGATGAACATGATGATGACAGGAGAAGGGCATTGCATGAAGAGTCAACACGCTGGAACCGAGTGGGTAT (SEQ ID NO: 15) PrimerGGCAGCAGACGATGAACATGATGAT CGCTGGAACCGAGTGGGTAT (SEQ ID NO: 16) DetectorGACAGGAGAAGGGCATTGCA (SEQ ID NO: 17) Capture TTGCATGAAGAGTCAACA(SEQ ID NO: 18) Blocking Pieces —

FIG. 21( a)-(b) shows the effects of these strategies on signals for theVEE 5′UTR and NSP4 targets. The figures show that the use of blockingsequences to block secondary structure formation was effective and couldproduce an assay signal increase of 2 to 5 fold. The second approach ofshortening the amplicon produced a 100 fold increase in assay signal. Weimplemented the amplicon shortening approach for the VEE assay.

Performance of 16-Plex ECL Hybridization Assay in Multi-Well PlateFormat. FIG. 22( a-b) demonstrates the performance of our optimized16-plex ECL sandwich hybridization assays in the multi-well plateformat. To be able to correlate results to the number of target sequencecopies, these results were generated using samples containing syntheticversions of our 16 gene targets. Detection limits were generally in therange of roughly 10⁶ to 10⁷ copies (assay volumes were about 100 uL).These detection limits are significantly lower than the amount ofamplified product that should be generated from a single copy based onour 15 minute, 45 cycle PCR protocol. Based on our calculated per cycleamplification efficiency (about 1.7 or greater), a single copy shouldgenerate ˜1.7⁴⁵=2×10¹⁰ copies of amplified product. FIG. 22 (a-b) alsoshows the observed levels of cross-reactivity of each target for thedifferent capture probes. In general, the levels of cross-reactivitywere below detectable levels. There were five instances where wedetected low levels of cross-reactivity (on the order of 1%) of a targetfor a non-specific capture probe and some additional optimization can berequired.

Performance of Multiplexed ECL Hybridization Assay in Cartridge Format.FIG. 23( a)-(b) shows ECL signals for measuring amplicons from a model6-plex panel (our 6 genetic targets for BA, FT and YP). We amplified 1pg of genomic DNA from BA, FT or YP using 33 cycles of amplification ona Robocycler thermocycler, followed by quenching of the Taq enzyme withEDTA and denaturation of double stranded product at 95° C. The denaturedproduct was combined with detection probes for the six target sequencesand loaded onto an immunoassay cartridge holding an array of captureprobes for the same targets. The remaining process steps (incubationwith the capture probe array, washing of the array with an ECL readbuffer and measurement of ECL) were carried out automatically using animmunoassay reader. To test reaction kinetics, we programmed the readerto vary incubation times from 1 to 15 minutes. We also ran serialdilutions of the samples using a 10 minute incubation to characterizethe dilution linearity for the measurement. The graph in FIG. 23( a)shows that by 5 minutes of incubation, assays signals were orders ofmagnitude above the background measured on a negative control (BSA)assay spot. Discrimination of signal from background was possible evenwith incubation times as short as 1 min. The table in FIG. 23( b) showsthat (for the 10 minute incubation time) the amplification productscould be diluted as much as 100-fold and still produce signalssignificantly above background. In general, the assays signals droppedlinearly with dilution, although the signals for some of the assays weresaturated for the neat sample. The ability to get signals orders ofmagnitude above background in a cartridge flow cell using a 5 minuteincubation suggest little risk in porting the final 16-plex assays tocartridge electrodes.

The present invention is not to be limited in scope by the specificembodiments described herein. Indeed, various modifications of theinvention in addition to those described herein will become apparent tothose skilled in the art from the foregoing description and accompanyingfigures. Such modifications are intended to fall within the scope of theclaims. Various publications are cited herein, the disclosures of whichare incorporated by reference in their entireties.

1. An assay cartridge for conducting a PCR analysis of a sample, saidcartridge comprising a chamber and a fluidic network including (a) aprimary flow path comprising, from a proximate to a distal end, aninlet, a purification zone, a PCR reaction zone, and a detection zone,wherein said primary flow path further comprises one or more air ventports, and (b) one or more fluidic conduits each intersecting saidprimary flow path and fluidically connected to said chamber, whereinsaid chamber is connected to an additional air vent port, and said PCRreaction zone comprises a first temperature controlled zone and a secondtemperature controlled zone and said fluidic network is configured toshuttle a metered volume of fluid between said first and secondtemperature controlled zones during a PCR reaction conducted in said PCRreaction zone.
 2. The assay cartridge of claim 1 wherein said reactionzone further comprises a restriction zone positioned between said firstand second reaction temperature controlled zones.
 3. The assay cartridgeof claim 1, wherein a fluidic conduit of said one or more fluidicconduits comprises a multi-conduit fluidic junction including (i) afirst conduit connecting said primary flow path and said chamber, and(ii) a second conduit connecting said chamber to said additional airvent port, wherein said fluidic conduit is in communication with anoptical fluid sensor at a position distal from said fluidic junction andsaid metered volume of fluid is defined by the distance between saidfluidic junction and said distal position.
 4. The assay cartridge ofclaim 3, wherein said multi-conduit fluidic junction is a three-wayjunction.
 5. The assay cartridge of claim 1 wherein said assay cartridgefurther comprises a plurality of chambers selected from a samplechamber, a reagent chamber, a PCR reagent chamber, a reconstitutionchamber, a waste chamber, and a mixing chamber.
 6. The assay cartridgeof claim 5 wherein said assay cartridge further comprises a samplechamber, a plurality of reagent chambers, a plurality of PCR reagentchambers, a plurality of reconstitution chambers, a waste chamber, and amixing chamber.
 7. The assay cartridge of claim 6 wherein said primaryflow path is intersected by a sample chamber multi-conduit fluidicjunction including (i) a first sample chamber conduit connecting saidprimary flow path and said sample chamber; and (ii) a second samplechamber conduit connecting said sample chamber to a sample chamber airvent port, wherein said sample chamber fluidic junction is incommunication with a sample chamber optical fluid sensor at a positiondistal from said sample chamber fluidic junction and said metered volumeof fluid is defined by the distance between said sample chamber fluidicjunction and said distal position.
 8. The assay cartridge of claim 7wherein said primary flow path is intersected by a mixing chambermulti-conduit fluidic junction including (i) a first mixing chamberconduit connecting said primary flow path and said mixing chamber; and(ii) a second mixing chamber conduit connecting said mixing chamber to amixing chamber air vent port, wherein said mixing chamber fluidicjunction is in communication with a mixing chamber optical fluid sensorat a position distal from said mixing chamber fluidic junction and saidmetered volume of fluid is defined by the distance between said mixingchamber fluidic junction and said distal position.
 9. The assaycartridge of claim 8 wherein said primary flow path further comprises aseries of Z-transitions at a position distal from said mixing chamberfluidic junction.
 10. The assay cartridge of claim 1 wherein saidpurification zone is fluidically connected to a first waste chamber anda purification reagent chamber.
 11. The assay cartridge of claim 10wherein purification zone comprises, from a proximal to a distal end,(i) a purification multi-conduit fluidic junction including (a) a firstpurification reagent chamber conduit connecting said primary flow pathand said purification reagent chamber; and (b) a second purificationreagent chamber conduit connecting said purification reagent chamber anda purification reagent chamber air vent port; (ii) an integratedpurification membrane positioned in said primary flow path of saidpurification zone; and (iii) a waste multi-conduit fluidic junctionincluding (a) a first waste chamber conduit connecting said primary flowpath and said waste chamber; and (b) a second waste chamber conduitconnecting said waste chamber and a waste chamber air vent port.
 12. Theassay cartridge of claim 11 wherein said purification zone comprises anintegrated purification membrane positioned on a support frit.
 13. Theassay cartridge of claim 11 wherein said integrated purificationmembrane is compressed prior to cartridge assembly.
 14. The assaycartridge of claim 11 wherein said integrated purification membranecomprises a glass fiber membrane.
 15. The assay cartridge of claim 11wherein said membrane has a retention volume of less than 10 uL.
 16. Theassay cartridge of claim 11 wherein said membrane has a retention volumeof less than 5 uL.
 17. The assay cartridge of claim 11 wherein saidmembrane has a retention volume of less than 2 uL.
 18. The assaycartridge of claim 11 wherein said purification zone further comprises apre-heating zone preceding said integrated purification membrane. 19.The assay cartridge of claim 11 wherein said purification zone comprisesan additional temperature controlled zone.
 20. The assay cartridge ofclaim 1 wherein said primary flow path is intersected at said reactionzone by one or more reagent multi-conduit junctions connecting (i) saidprimary flow path and one or more reaction reagent chambers; and (ii)said one or more reagent chambers and one or more reagent chamber airvent ports.
 21. The assay cartridge of claim 20 wherein said assaycartridge further comprises one or more reconstitution chambers and saidone or more reagent multi-conduit junctions further connect (iii) saidprimary flow path and said one or more reconstitution chambers at saidreaction zone.
 22. The assay cartridge of claim 20 wherein said reactionzone comprises a reaction zone inlet and a reaction zone outlet, andsaid one or more multi-conduit junctions intersect said reaction zone atsaid reaction zone inlet and/or outlet.
 23. The assay cartridge of claim1 wherein said reaction zone comprises a first reaction temperaturecontrolled zone and a second reaction temperature controlled zone andsaid fluidic network is configured to shuttle a volume of fluid betweensaid first and second reaction temperature controlled zones during areaction conducted in said reaction zone.
 24. The assay cartridge ofclaim 23 wherein said reaction zone further comprises a restriction zonebetween said first and second reaction temperature controlled zones. 25.The assay cartridge of claim 1 wherein said primary flow path isintersected at said detection zone by a detection reagent multi-conduitjunction connecting (i) said primary flow path and one or more detectionreagent chambers; and (ii) said one or more detection reagent chambersand one or more detection reagent air vent ports.
 26. The assaycartridge of claim 25 wherein said detection zone comprises a set ofimmobilized reagents distributed in said detection zone along saidprimary flow path.
 27. The assay cartridge of claim 26 wherein saiddetection zone further comprises an exposed working electrode on whichsaid reagents are immobilized.
 28. The assay cartridge of claim 25wherein said detection zone is configured to maintain uniform fluid flowthroughout said detection zone.
 29. The assay cartridge of claim 25wherein said detection zone comprises a square geometry.
 30. The assaycartridge of claim 25 wherein said primary flow path is U-shaped withinsaid detection zone.
 31. The assay cartridge of claim 1 wherein saiddetection zone further comprises a detection temperature controlledzone.
 32. The assay cartridge of claim 1 wherein one or more of saidchambers comprise a liquid reagent.
 33. The assay cartridge of claim 1wherein one or more of said chambers comprise a dried reagent that canbe rehydrated by said metered volume of fluid.
 34. The assay cartridgeof claim 1 wherein the surface of said primary flow path within saidpurification zone and/or said reaction zone is substantially adhesivefree.
 35. The assay cartridge of claim 1 wherein the surface of saidprimary flow path within said purification zone and/or said reactionzone is substantially free of seams.
 36. The assay cartridge of claim 1wherein said mixing chamber is configured to perform cell lysis.
 37. Theassay cartridge of claim 36 wherein said mixing chamber is in fluidiccommunication with said sample chamber and said reagent chamber, andsaid reagent chamber comprises a lysis reagent.
 38. The assay cartridgeof claim 37 wherein said mixing chamber further comprises an antifoamreagent.
 39. The assay cartridge of claim 1 wherein said purificationzone is configured to extract and purify nucleic acids in said sample.40. The assay cartridge of claim 39 wherein said purification zone is influidic communication with a plurality of reagent chambers eachcomprising a lysis buffer, a wash buffer, and an elution buffer.
 41. Theassay cartridge of claim 40 wherein each of said reconstitution chamberscomprise lyophilized PCR reagents.
 42. The assay cartridge of claim 41wherein said PCR reagents comprise reverse transcriptase, dNTPs, andcombinations thereof.
 43. The assay cartridge of claim 42 wherein saidPCR reagents are housed within a first reconstitution chamber.
 44. Theassay cartridge of claim 41 wherein said PCR reagents are selected fromdNTPs, primers, polymerase, and combinations thereof.
 45. The assaycartridge of claim 44 wherein said PCR reagents are housed within asecond reconstitution chamber.
 46. The assay cartridge of claim 41wherein said PCR reagents comprise additional primers.
 47. The assaycartridge of claim 46 wherein said PCR reagents are housed within athird reconstitution chamber.
 48. The assay cartridge of claim 41wherein said PCR reagents are selected from EDTA, salt, and combinationsthereof.
 49. The assay cartridge of claim 48 wherein said PCR reagentsare housed within a fourth reconstitution chamber.
 50. The assaycartridge of claim 41 wherein said PCR reagents comprise detectionprobes.
 51. The assay cartridge of claim 50 wherein said PCR reagentsare housed within a fifth reconstitution chamber.
 52. A method ofconducting a PCR analysis of a sample in an assay cartridge, saidcartridge comprising a fluidic network and a plurality of chambers,wherein said fluidic network comprises (a) a primary flow pathcomprising, from a proximate to a distal end, (i) an inlet, (ii) apurification zone, (iii) a PCR reaction zone including a first reactiontemperature controlled zone and a second reaction temperature controlledzone, and (iv) a detection zone, wherein said primary flow path furthercomprises (vi) one or more air vent ports, and (b) one or more fluidicconduits each intersecting said primary flow path and fluidicallyconnected to one or more of said chambers, wherein each of said chambersare connected to an additional air vent port, wherein said plurality ofchambers include: a sample chamber, a lysis reagent chamber, a lysischamber, a purification reagent chamber, a plurality of PCR reagentchambers, and one or more waste chambers; said method comprising thesteps of: (i) metering a volume of sample from said sample chamber tosaid lysis chamber; (ii) metering a volume of lysis buffer from saidlysis reagent chamber to said lysis chamber; (iii) lysing said volume ofsample; (iv) moving said lysate from said lysis chamber to saidpurification zone; (v) extracting nucleic acid from said lysate; (vi)purifying said nucleic acid; (vii) moving said a purified nucleic acidmixture to said PCR reaction zone; (viii) contacting said purifiednucleic acid mixture with one or more PCR reagents; (ix) shuttling saidmixture formed in step (viii) between said first and second temperaturecontrolled zones; (ix) repeating steps (viii) and (ix) to form anamplified product mixture; (x) contacting said amplified product mixturewith a detection reagent; (xi) moving said mixture formed in step (x) tosaid detection zone; and (xii) measuring a signal from said detectionzone.
 53. The method of claim 52, wherein said purification zonecomprises, from a proximal to a distal end, (i) a purificationmulti-conduit fluidic junction including (a) a first purificationreagent chamber conduit connecting said primary flow path and saidpurification reagent chamber; and (b) a second purification reagentchamber conduit connecting said purification reagent chamber and apurification reagent chamber air vent port; (ii) an integratedpurification membrane positioned in said primary flow path of saidpurification zone; and (iii) a waste multi-conduit fluidic junctionincluding (a) a first waste chamber conduit connecting said primary flowpath and said waste chamber; and (b) a second waste chamber conduitconnecting said waste chamber and a waste chamber air vent port; andsaid extracting step (v) comprises (xx) capturing lysate on saidmembrane; (yy) removing eluent to said first waste chamber; and (zz)washing said membrane with one or more purification reagents.
 54. Themethod of claim 43 wherein said purifying step (vi) comprises (xx)drying said membrane; (yy) washing said membrane with purificationreagent; and (zz) eluting nucleic acid from said membrane.
 55. Themethod of claim 52 wherein said cartridge further comprises a pluralityof reconstitution chambers each comprising lyophilized PCR reagents andcontacting step (viii) further comprises reconstituting one or more ofsaid lyophilized PCR reagents.
 56. The method of claim 55 wherein saidcartridge further comprises a first reconstitution chamber comprising afirst set of PCR reagents selected from reverse transcriptase and dNTPs,and said method further comprises reconstituting said first set of PCRreagents in said contacting step (viii) and shuttling said mixtureformed in said contacting step between said first and second temperaturecontrolled zone.
 57. The method of claim 56 wherein said cartridgefurther comprises a second reconstitution chamber comprising a secondset of PCR reagents selected from dNTPs, primers, and polymerase, andsaid method further comprises reconstituting said second set of PCRreagents in said contacting step (viii) and shuttling said mixtureformed in said contacting step between said first and second temperaturecontrolled zone.
 58. The method of claim 57 wherein said cartridgefurther comprises a third reconstitution chamber comprising a third setof PCR reagents comprising additional primers, and said method furthercomprises reconstituting said third set of PCR reagents in saidcontacting step (viii) and shuttling said mixture formed in saidcontacting step between said first and second reaction temperaturecontrolled zone.
 59. The method of claim 58 wherein said cartridgefurther comprises a fourth reconstitution chamber comprising a fourthset of PCR reagents selected from EDTA, and salt, and said methodfurther comprises reconstituting said fourth set of PCR reagents in saidcontacting step (viii) and shuttling said mixture formed in saidcontacting step between said first and second reaction temperaturecontrolled zone.
 60. The method of claim 59 wherein said cartridgefurther comprises a fifth reconstitution chamber comprising detectionreagents and said contacting step (x) comprises reconstituting saiddetection reagents with said amplified product mixture.
 61. A fluidicnetwork comprising a chamber connected to an air vent port, said fluidicnetwork comprising a primary flow path and one or more fluidic conduitseach intersecting said primary flow path and fluidically connecting saidprimary flow path to said chamber, wherein said fluidic network isconfigured to meter a volume of fluid in said network.
 62. The fluidicnetwork of claim 61, wherein a fluidic conduit of said one or morefluidic conduits comprises a multi-conduit fluidic junction including(i) a first conduit connecting said primary flow path and said chamber,and (ii) a second conduit connecting said chamber to said air vent port,wherein said fluidic conduit is in communication with an optical fluidsensor at a position distal from said fluidic junction and said meteredvolume of fluid is defined by the distance between said fluidic junctionand said distal position.
 63. The fluidic network of claim 61, whereinsaid multi-conduit fluidic junction is a three-way junction.
 64. Asystem configured to interface with a fluidic network of claim 61, saidsystem comprising a fluidic control manifold configured to drive fluidmotion within said fluidic network.
 65. The system of claim 64 whereinsaid fluidic control manifold comprises a pump and a pressure sensor andsaid system is configured to align said fluidic control manifold withone or more air vent ports positioned in said fluidic network.